openbel-api 1.2.6-java → 1.2.7-java

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (14) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +2 -0
  3. data/VERSION +1 -1
  4. data/app/openbel/api/helpers/nanopub.rb +159 -0
  5. data/app/openbel/api/resources/completion.rb +3 -2
  6. data/app/openbel/api/routes/base.rb +1 -1
  7. data/app/openbel/api/routes/datasets.rb +33 -22
  8. data/app/openbel/api/routes/nanopubs.rb +2 -158
  9. data/bin/bel2.0-example-statements.bel +344 -0
  10. data/bin/bel2_document_examples.bel +250 -0
  11. data/bin/test_bel2_validation.py +68 -0
  12. data/bin/test_results.json +2208 -0
  13. data/config/config.yml +1 -1
  14. metadata +10 -2
data/bin/bel2.0-example-statements.bel ADDED
@@ -0,0 +1,344 @@
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+ a(CHEBI:"2-oxoglutarate(2-)") directlyIncreases act(p(HGNC:EGLN1), ma(GO:"catalytic activity"))
2
+ a(CHEBI:"3',5'-cyclic AMP") increases act(p(HGNC:RAP1A))
3
+ a(CHEBI:"3',5'-cyclic GMP") increases surf(complex(p(HGNC:ITGAV),p(HGNC:ITGB5)))
4
+ a(CHEBI:"arachidonic acid") increases act(p(MGI:Mpo), ma(DEFAULT:cat))
5
+ a(CHEBI:"fatty acid") increases act(p(HGNC:UCP1))
6
+ a(CHEBI:"nitric oxide") increases act(p(SFAM:"GUCY Family"), ma(GO:"catalytic activity"))
7
+ a(CHEBI:"nitric oxide") decreases r(HGNC:CFTR, var("c.1521_1523delCTT"))
8
+ a(CHEBI:"nitric oxide") increases surf(complex(p(HGNC:ITGA2),p(HGNC:ITGB1)))
9
+ a(CHEBI:"okadaic acid") directlyDecreases act(complex(SCOMP:"PP2A Complex"), ma(GO:"phosphatase activity"))
10
+ a(CHEBI:"okadaic acid") increases p(HGNC:IRS1,pmod(Ph,Ser))
11
+ a(CHEBI:"oxidised LDL") increases act(p(HGNC:MMP2), ma(DEFAULT:cat))
12
+ a(CHEBI:"oxidised LDL") increases surf(p(HGNC:MMP14))
13
+ a(CHEBI:"phosphatidyl-L-serine") increases act(p(HGNC:F3), ma(GO:"peptidase activity"))
14
+ a(CHEBI:"phosphatidyl-L-serine") increases act(p(SFAM:"PDE4 Long Family"), ma(GO:"catalytic activity"))
15
+ a(CHEBI:"prostaglandin E2") increases act(p(HGNC:RAP1A))
16
+ a(CHEBI:"prostaglandin E2") decreases p(HGNC:PRKCD,pmod(Ph))
17
+ a(CHEBI:acetylcholine) increases act(p(HGNC:NOS3), ma(DEFAULT:cat))
18
+ a(SCHEM:"LY 294002") causesNoChange act(p(HGNC:MAPK1), ma(DEFAULT:kin))
19
+ act(complex(p(HGNC:CCND1),p(HGNC:CDK4)), ma(DEFAULT:kin)) directlyIncreases p(HGNC:RB1,pmod(Ph))
20
+ act(complex(p(HGNC:F3),p(HGNC:F7)), ma(GO:"peptidase activity")) directlyIncreases act(p(HGNC:F10), ma(DEFAULT:pep))
21
+ act(complex(SCOMP:"Calcineurin Complex"), ma(GO:"phosphatase activity")) increases act(p(SFAM:"MEF2 Family"), ma(GO:"nucleic acid binding transcription factor activity"))
22
+ act(complex(SCOMP:"Calcineurin Complex"), ma(GO:"phosphatase activity")) causesNoChange r(MGI:Ppargc1a)
23
+ act(complex(SCOMP:"IkappaB Kinase Complex"), ma(DEFAULT:kin)) increases act(complex(SCOMP:"Nfkb Complex"), ma(DEFAULT:tscript))
24
+ act(complex(SCOMP:"IkappaB Kinase Complex"), ma(DEFAULT:kin)) directlyIncreases deg(p(HGNC:NFKBIA))
25
+ act(complex(SCOMP:"p85/p110 PI3Kinase Complex"), ma(DEFAULT:kin)) increases surf(p(HGNC:ATP1A2,pmod(Ph,Thr)))
26
+ act(complex(SCOMP:"PP2A Complex"), ma(GO:"phosphatase activity")) increases bp(MESHPP:"Capillary Permeability")
27
+ act(complex(SCOMP:"PP2A Complex"), ma(GO:"phosphatase activity")) directlyDecreases p(HGNC:RAF1,pmod(Ph,S))
28
+ act(complex(SCOMP:"PP2A Complex"), ma(GO:"phosphatase activity")) directlyDecreases p(HGNC:RAF1,pmod(Ph,S,259))
29
+ act(complex(SCOMP:"TORC1 Complex"), ma(DEFAULT:kin)) directlyIncreases p(MGI:Rps6kb1,pmod(Ph,Thr,412))
30
+ act(complex(SCOMP:"TORC2 Complex"), ma(DEFAULT:kin)) directlyIncreases p(MGI:Eif4ebp1,pmod(Ph,Thr,36))
31
+ act(p(fus(HGNC:BCR,?, HGNC:ABL1,?))) increases act(complex(SCOMP:"p85/p110 PI3Kinase Complex"), ma(DEFAULT:kin))
32
+ act(p(fus(HGNC:BCR,?, HGNC:ABL1,?))) increases bp(GOBP:"cell adhesion")
33
+ act(p(fus(HGNC:BCR,?, HGNC:ABL1,?))) increases p(HGNC:FOXO3,pmod(Ph,Ser,253))
34
+ act(p(fus(HGNC:EWSR1,?, HGNC:FLI1,?))) directlyDecreases r(HGNC:CDKN1A)
35
+ act(p(fus(HGNC:PAX3,?,HGNC:FOXO1,?)), ma(DEFAULT:tscript)) decreases r(HGNC:IGFBP5)
36
+ act(p(fus(HGNC:TPR,?, HGNC:MET,?))) increases path(SDIS:"tumor growth")
37
+ act(p(HGNC:"NKX2-5"), ma(DEFAULT:tscript)) directlyIncreases r(HGNC:MIR143)
38
+ act(p(HGNC:ADAMTS13), ma(GO:"peptidase activity")) increases deg(p(HGNC:VWF))
39
+ act(p(HGNC:AKT1), ma(DEFAULT:kin)) decreases act(p(HGNC:FOXO3), ma(GO:"nucleic acid binding transcription factor activity"))
40
+ act(p(HGNC:AKT1), ma(DEFAULT:kin)) increases act(p(HGNC:MDM2), ma(DEFAULT:cat))
41
+ act(p(HGNC:AKT1), ma(DEFAULT:kin)) directlyDecreases act(p(HGNC:PAWR))
42
+ act(p(HGNC:AKT1), ma(DEFAULT:kin)) directlyDecreases act(p(SFAM:"FOXO Family"), ma(GO:"nucleic acid binding transcription factor activity"))
43
+ act(p(HGNC:AKT1), ma(DEFAULT:kin)) decreases complex(p(HGNC:AKT1),p(HGNC:CREBBP))
44
+ act(p(HGNC:AKT1), ma(DEFAULT:kin)) increases complex(p(HGNC:SKP2),p(SFAM:"FOXO Family"))
45
+ act(p(HGNC:AKT1), ma(DEFAULT:kin)) increases tloc(p(HGNC:CDKN1A), fromLoc(MESHCS:"Cell Nucleus"), toLoc(MESHCS:Cytoplasm))
46
+ act(p(HGNC:AKT1), ma(DEFAULT:kin)) decreases tloc(p(SFAM:"FOXO Family"), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus"))
47
+ act(p(HGNC:CASP3), ma(GO: "catalytic activity")) decreases act(p(HGNC:PARP1), ma(DEFAULT:ribo))
48
+ act(p(HGNC:CDK1), ma(DEFAULT:kin)) directlyIncreases act(complex(SCOMP:"Anaphase Promoting Complex"), ma(GO: "catalytic activity"))
49
+ act(p(HGNC:CDK2), ma(DEFAULT:kin)) directlyIncreases p(HGNC:CDKN1B,pmod(Ph,Thr,187))
50
+ act(p(HGNC:CTNNB1), ma(DEFAULT:tscript)) directlyIncreases r(HGNC:CCND1)
51
+ act(p(HGNC:CYP7A1), ma(DEFAULT:cat)) rateLimitingStepOf deg(a(CHEBI:cholesterol))
52
+ act(p(HGNC:EGLN3), ma(DEFAULT:cat)) directlyIncreases p(HGNC:HIF1A,pmod(Hy,Pro,564))
53
+ act(p(HGNC:F2), ma(GO:"peptidase activity")) directlyIncreases act(p(HGNC:F2R))
54
+ act(p(HGNC:F2), ma(GO:"peptidase activity")) increases bp(GOBP:"blood coagulation")
55
+ act(p(HGNC:F9), ma(DEFAULT:pep)) increases act(p(HGNC:F2), ma(GO:"peptidase activity"))
56
+ act(p(HGNC:HIF1AN), ma(GO:"catalytic activity")) directlyIncreases p(HGNC:HIF1A,pmod(Hy,Asn,803))
57
+ act(p(HGNC:HMGA1)) increases surf(p(HGNC:INSR))
58
+ act(p(HGNC:HMOX1), ma(DEFAULT:cat)) directlyIncreases rxn(reactants(a(CHEBI:heme)),products(a(SCHEM:Biliverdine),a(CHEBI:"carbon monoxide")))
59
+ act(p(HGNC:HRAS), ma(DEFAULT:gtp)) increases surf(p(HGNC:CDH5))
60
+ act(p(HGNC:JUN), ma(GO:"nucleic acid binding transcription factor activity")) increases path(MESHD:"Carcinoma, Squamous Cell")
61
+ act(p(HGNC:JUN), ma(GO:"nucleic acid binding transcription factor activity")) increases path(SDIS:"tumor growth")
62
+ act(p(HGNC:KDR), ma(GO:"kinase activity")) directlyIncreases p(HGNC:KDR,pmod(Ph,Y,951))
63
+ act(p(HGNC:KDR), ma(GO:"kinase activity")) directlyIncreases p(HGNC:KDR,pmod(Ph,Y,996))
64
+ act(p(HGNC:KDR), ma(DEFAULT:kin)) association bp(GOBP:"cell death")
65
+ act(p(HGNC:KLF9), ma(DEFAULT:tscript)) association bp(GOBP:"DNA replication")
66
+ act(p(HGNC:LEF1), ma(DEFAULT:tscript)) directlyIncreases r(HGNC:CCND1)
67
+ act(p(HGNC:MAP2K1), ma(DEFAULT:kin)) increases surf(p(HGNC:ITGB3))
68
+ act(p(HGNC:MYD88), ma(GO:"catalytic activity")) directlyIncreases complex(p(HGNC:MYD88),p(HGNC:IRAK1),p(HGNC:IRAK4))
69
+ act(p(HGNC:NAA10), ma(DEFAULT:cat)) directlyIncreases p(HGNC:HIF1A,pmod(Ac,K,532))
70
+ act(p(HGNC:PAK3), ma(GO:"kinase activity")) directlyIncreases p(HGNC:RAF1,pmod(Ph,S,338))
71
+ act(p(HGNC:PDPK1), ma(GO:"kinase activity")) directlyIncreases p(SFAM:"AKT Family",pmod(MOD:PhosRes,Tyr,308))
72
+ act(p(HGNC:PIM1)) increases surf(p(HGNC:KDR))
73
+ act(p(HGNC:PLCG1)) directlyIncreases rxn(reactants(a(SCHEM:"1-Phosphatidyl-D-myo-inositol 4,5-bisphosphate")),products(a(SCHEM:Diacylglycerol),a(SCHEM:"Inositol 1,4,5-trisphosphate")))
74
+ act(p(HGNC:PRKCZ), ma(GO:"kinase activity")) increases tloc(p(HGNC:SLC2A4), fromLoc(MESHCS:"Intracellular Space"), toLoc(MESHCS:"Cell Membrane"))
75
+ act(p(HGNC:PTEN), ma(DEFAULT:phos)) decreases act(p(HGNC:AKT1), ma(DEFAULT:kin))
76
+ act(p(HGNC:PTPRJ), ma(DEFAULT:phos)) directlyDecreases act(p(HGNC:KDR), ma(DEFAULT:kin))
77
+ act(p(HGNC:RANBP2), ma(GO:"catalytic activity")) directlyIncreases p(HGNC:HDAC4,pmod(Sumo,Lys,559))
78
+ act(p(HGNC:ROCK1), ma(DEFAULT:kin)) association path(SDIS:"cardiomyocyte hypertrophy")
79
+ act(p(HGNC:SGK1), ma(DEFAULT:kin)) directlyIncreases p(HGNC:RAF1,pmod(Ph,S,259))
80
+ act(p(HGNC:SOD2), ma(DEFAULT:cat)) increases rxn(reactants(a(CHEBI:superoxide)),products(a(CHEBI:"hydrogen peroxide")))
81
+ act(p(HGNC:SRC), ma(DEFAULT:kin)) increases act(p(SFAM:"RAF Family"), ma(GO:"kinase activity"))
82
+ act(p(HGNC:SRC), ma(DEFAULT:kin)) directlyIncreases p(HGNC:CDH5,pmod(Ph,Y))
83
+ act(p(HGNC:SRF), ma(DEFAULT:tscript)) directlyIncreases r(HGNC:MIR143)
84
+ act(p(HGNC:TIMP2), ma(DEFAULT:pep)) decreases p(HGNC:MMP9)
85
+ act(p(HGNC:TNFRSF1A)) regulates act(complex(SCOMP:"AP-1 Complex"), ma(DEFAULT:tscript))
86
+ act(p(HGNC:TNFRSF1A)) increases act(p(SFAM:"PRKC Family"), ma(GO:"kinase activity"))
87
+ act(p(HGNC:USF1), ma(DEFAULT:tscript)) causesNoChange r(HGNC:IGF2R)
88
+ act(p(HGNC:VHL), ma(DEFAULT:cat)) directlyIncreases deg(p(HGNC:PRKCI))
89
+ act(p(MGI:Akt1), ma(DEFAULT:kin)) directlyDecreases act(p(SFAM:"FOXO Family"), ma(GO:"nucleic acid binding transcription factor activity"))
90
+ act(p(MGI:Akt1), ma(DEFAULT:kin)) directlyIncreases p(MGI:Foxo3,pmod(Ph,Thr,32))
91
+ act(p(MGI:Akt1), ma(DEFAULT:kin)) directlyIncreases p(MGI:Tsc2,pmod(Ph,Ser,939))
92
+ act(p(MGI:Akt1), ma(DEFAULT:kin)) decreases r(MGI:Cdkn1b)
93
+ act(p(MGI:Cebpd), ma(DEFAULT:tscript)) association bp(MESHPP:Apoptosis)
94
+ act(p(MGI:Chuk), ma(DEFAULT:kin)) increases deg(p(MGI:Nfkbia))
95
+ act(p(MGI:Ctnnb1), ma(GO:"nucleic acid binding transcription factor activity")) increases r(MGI:Myc)
96
+ act(p(MGI:Epas1), ma(DEFAULT:tscript)) increases surf(complex(p(MGI:Itgav),p(MGI:Itgb3)))
97
+ act(p(MGI:Fads1), ma(GO: "catalytic activity")) directlyIncreases rxn(reactants(a(CHEBI:"all-cis-icosa-8,11,14-trienoic acid")),products(a(CHEBI:"arachidonic acid")))
98
+ act(p(MGI:Fads2), ma(GO: "catalytic activity")) increases a(CHEBI:"arachidonic acid")
99
+ act(p(MGI:Foxp3), ma(DEFAULT:tscript)) decreases sec(p(MGI:Ifng))
100
+ act(p(MGI:Hif1a), ma(DEFAULT:tscript)) increases bp(GOBP:angiogenesis)
101
+ act(p(MGI:Hras,var("p.Gly12Val")), ma(DEFAULT:gtp)) increases act(complex(SCOMP:"NADPH Oxidase Complex"), ma(GO:"catalytic activity"))
102
+ act(p(MGI:Ikbkb), ma(DEFAULT:kin)) increases deg(p(MGI:Nfkbia))
103
+ act(p(MGI:Inppl1), ma(DEFAULT:phos)) negativeCorrelation path(MESHD:Hyperglycemia)
104
+ act(p(MGI:Itch), ma(DEFAULT:cat)) directlyIncreases deg(p(MGI:Trp63))
105
+ act(p(MGI:Lpl), ma(DEFAULT:cat)) rateLimitingStepOf path(SDIS:"VLDL biosynthesis")
106
+ act(p(MGI:Mmp2), ma(DEFAULT:cat)) rateLimitingStepOf bp(GOBP:"cellular extravasation")
107
+ act(p(MGI:Mtor), ma(DEFAULT:kin)) directlyIncreases p(MGI:Eif4ebp1,pmod(Ph,Thr,36))
108
+ act(p(MGI:Mybl1), ma(DEFAULT:tscript)) association bp(GOBP:"G1/S transition of mitotic cell cycle")
109
+ act(p(MGI:Ppargc1a), ma(DEFAULT:tscript)) directlyIncreases act(p(SFAM:"MEF2 Family"), ma(DEFAULT:tscript))
110
+ act(p(MGI:Tcf3), ma(DEFAULT:tscript)) directlyIncreases r(MGI:Bmp4)
111
+ act(p(MGI:Tlr2), ma(DEFAULT:cat)) increases sec(p(MGI:Ccl2))
112
+ act(p(RGD:Hmox1), ma(DEFAULT:cat)) rateLimitingStepOf deg(a(CHEBI:heme))
113
+ act(p(SFAM:"ACSL Family"), ma(GO: "catalytic activity")) directlyIncreases rxn(reactants(a(SCHEM:"Long-chain fatty acid")),products(a(SCHEM:"Long-chain fatty acyl CoA")))
114
+ act(p(SFAM:"AKT Family"), ma(DEFAULT:kin)) directlyIncreases p(HGNC:GSK3B,pmod(MOD:PhosRes,Ser,9))
115
+ act(p(SFAM:"FOXO Family"), ma(GO:"nucleic acid binding transcription factor activity")) decreases bp(GOBP:"G1/S transition of mitotic cell cycle")
116
+ act(p(SFAM:"FOXO Family"), ma(DEFAULT:tscript)) directlyDecreases r(HGNC:CCND1)
117
+ act(p(SFAM:"JAK Family"), ma(GO:"kinase activity")) directlyIncreases p(HGNC:RAF1,pmod(Ph,Tyr,341))
118
+ act(p(SFAM:"MAPK Erk1/2 Family"), ma(GO:"kinase activity")) directlyIncreases p(HGNC:PDE4B,pmod(Ph,Ser))
119
+ act(p(SFAM:"MAPK JNK Family"), ma(GO:"kinase activity")) increases tloc(p(HGNC:CYCS), fromLoc(MESHCS:"Mitochondrial Membranes"), toLoc(MESHCS:Cytoplasm))
120
+ act(p(SFAM:"MAPK p38 Family"), ma(GO:"kinase activity")) decreases deg(p(HGNC:HBP1))
121
+ act(p(SFAM:"MAPK p38 Family"), ma(GO:"kinase activity")) directlyIncreases p(HGNC:CDKN1A,pmod(Ph,Ser,190))
122
+ act(p(SFAM:"MAPK p38 Family"), ma(GO:"kinase activity")) directlyIncreases p(HGNC:HBP1,pmod(Ph))
123
+ act(p(SFAM:"NOS Family"), ma(DEFAULT:cat)) increases rxn(reactants(a(CHEBI:dioxygen),a(CHEBI:"L-arginine")),products(a(CHEBI:"nitric oxide")))
124
+ act(p(SFAM:"PDE Family"), ma(GO: "catalytic activity")) directlyIncreases rxn(reactants(a(CHEBI:"3',5'-cyclic AMP")),products(a(CHEBI:AMP)))
125
+ act(p(SFAM:"PRKA Family"), ma(GO:"kinase activity")) directlyDecreases act(p(HGNC:GSK3B), ma(DEFAULT:kin))
126
+ act(p(SFAM:"PRKA Family"), ma(GO:"kinase activity")) directlyIncreases act(p(SFAM:"PDE4 Long Family"), ma(GO: "catalytic activity"))
127
+ act(p(SFAM:"PRKA Family"), ma(GO:"kinase activity")) directlyIncreases p(HGNC:CREB1,pmod(Ph,Ser,133))
128
+ act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases act(complex(SCOMP:"p85/p110 PI3Kinase Complex"), ma(GO:"kinase activity"))
129
+ act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases act(p(SFAM:"MAPK Erk1/2 Family"), ma(GO:"kinase activity"))
130
+ act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases act(p(SFAM:"RAC Family"), ma(DEFAULT:gtp))
131
+ act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) directlyIncreases act(p(SFAM:"RAF Family"), ma(GO:"kinase activity"))
132
+ act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases act(p(SFAM:"RHO Family"), ma(DEFAULT:gtp))
133
+ act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases bp(GOBP:"cell proliferation")
134
+ act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases complex(p(HGNC:RAF1),p(HGNC:BRAF))
135
+ act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) increases p(HGNC:RAF1,pmod(Ph,S,338))
136
+ act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) positiveCorrelation path(MESHD:"Carcinoma, Non-Small-Cell Lung")
137
+ act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp)) directlyIncreases tloc(p(HGNC:BRAF), fromLoc(MESHCS:"Intracellular Space"), toLoc(MESHCS:"Cell Membrane"))
138
+ act(p(SFAM:"SRC Family"), ma(GO:"kinase activity")) directlyIncreases p(HGNC:RAF1,pmod(Ph,Tyr,341))
139
+ bp(GOBP:"cellular response to electrical stimulus") increases tloc(p(MGI:Hdac4), fromLoc(MESHCS:"Cell Nucleus"), toLoc(MESHCS:Cytoplasm))
140
+ bp(GOBP:"mitotic nuclear division") positiveCorrelation p(HGNC:CDC16,pmod(Ph,Ser,558))
141
+ bp(GOBP:"mitotic nuclear division") positiveCorrelation p(HGNC:CDC23,pmod(Ph,Thr,556))
142
+ bp(GOBP:"response to endoplasmic reticulum") increases a(CHEBI:"calcium(2+)", loc(GOCC:"endoplasmic reticulum"))
143
+ bp(MESHPP:"Insulin Resistance") negativeCorrelation act(p(SFAM:"AKT Family"), ma(GO:"kinase activity"))
144
+ bp(MESHPP:Obesity) negativeCorrelation act(p(HGNC:SLC2A4), ma(DEFAULT:tport))
145
+ bp(MESHPP:Obesity) positiveCorrelation act(p(MGI:Trp53), ma(DEFAULT:tscript))
146
+ complex(p(HGNC:CTNNB1),p(HGNC:LEF1)) directlyIncreases act(p(HGNC:CTNNB1), ma(DEFAULT:tscript))
147
+ complex(p(HGNC:CYCS),p(HGNC:APAF1)) increases act(p(HGNC:CASP9), ma(GO:"peptidase activity"))
148
+ complex(p(HGNC:F3),p(HGNC:F7)) increases act(p(HGNC:F10), ma(DEFAULT:pep))
149
+ complex(p(HGNC:HIF1A),p(HGNC:EP300)) directlyIncreases act(p(HGNC:HIF1A), ma(DEFAULT:tscript))
150
+ complex(p(HGNC:ITGA6),p(HGNC:ITGB1)) increases act(p(HGNC:SYK), ma(DEFAULT:kin))
151
+ complex(p(HGNC:ITGB1),p(HGNC:FN1)) increases act(p(HGNC:PRKCA), ma(DEFAULT:kin))
152
+ complex(p(HGNC:MAP3K11),p(HGNC:SH3RF1)) increases act(p(SFAM:"MAPK JNK Family"), ma(GO:"kinase activity"))
153
+ complex(p(HGNC:MAP3K11),p(HGNC:SH3RF1)) increases p(HGNC:JUN,pmod(Ph))
154
+ complex(p(HGNC:RBL2),p(SFAM:"E2F Family")) decreases bp(GOBP:"G1/S transition of mitotic cell cycle")
155
+ complex(p(HGNC:RBL2),p(SFAM:"E2F Family")) directlyDecreases complex(p(SFAM:"E2F Family"),p(HGNC:EP300))
156
+ composite(a(SCHEM:Lipopolysaccharide),p(MGI:Ifng)) increases act(complex(SCOMP:"PP2A Complex"), ma(GO:"phosphatase activity"))
157
+ composite(p(HGNC:RAF1),p(HGNC:AKT1)) regulates act(p(HGNC:CDK2), ma(DEFAULT:kin))
158
+ composite(p(HGNC:VEGFA),p(HGNC:FN1)) increases act(p(HGNC:PRKCA), ma(DEFAULT:kin))
159
+ composite(p(HGNC:VEGFA),p(HGNC:FN1)) increases surf(p(HGNC:PRKCA))
160
+ g(REF:"NM_000492.3", var("c.1521_1523delCTT")) association bp(GOBP:"wound healing")
161
+ p(HGNC:AKT1, loc(MESHCS:Cytoplasm)) increases p(HGNC:EGFR, loc(MESHCS: Cytoplasm))
162
+ p(HGNC:APP, frag("?_*")) negativeCorrelation path(SDIS:"Alzheimers disease")
163
+ p(HGNC:APP, frag(25_35)) association path(SDIS:"Alzheimers disease")
164
+ p(HGNC:BCL2) causesNoChange act(p(HGNC:PAWR))
165
+ p(HGNC:BCL2, loc(MESHCS:Mitochondria)) increases p(HGNC:CYCS, loc(MESHCS:Mitochondria))
166
+ p(HGNC:BRAF,var("p.Val599Glu")) directlyIncreases act(p(HGNC:BRAF), ma(DEFAULT:kin))
167
+ p(HGNC:CALM1) regulates act(p(HGNC:NOS3), ma(DEFAULT:cat))
168
+ p(HGNC:CASP3) increases p(HGNC:APC, frag(1_?))
169
+ p(HGNC:CASP3) increases p(HGNC:HTT, frag(?))
170
+ p(HGNC:CASP8) increases p(HGNC:CFLAR, frag(?,36kD))
171
+ p(HGNC:CASP9, frag(?,55kD)) increases bp(GOBP:"apoptotic process")
172
+ p(HGNC:CAV1) directlyDecreases act(p(HGNC:KDR), ma(DEFAULT:kin))
173
+ p(HGNC:CAV1,pmod(Ph,Y,14)) directlyDecreases complex(p(HGNC:CAV1),p(HGNC:KDR))
174
+ p(HGNC:CDH5,pmod(Ph,Tyr)) directlyDecreases bp(GOBP:"single organismal cell-cell adhesion")
175
+ p(HGNC:CDKN1A,pmod(Ph,Ser,190)) decreases deg(p(HGNC:CDKN1A))
176
+ p(HGNC:CDKN1B,pmod(Ph,Thr,187)) directlyIncreases complex(p(HGNC:SKP2),p(HGNC:CDKN1B))
177
+ p(HGNC:CDKN1B,pmod(Ub)) directlyIncreases deg(p(HGNC:CDKN1B))
178
+ p(HGNC:CFTR, var("?"")) regulates p(HGNC:NFKBIA)
179
+ p(HGNC:CFTR, var("="")) increases act(p(HGNC:SLC9A3))
180
+ p(HGNC:CFTR, var("p.Phe508del")) decreases bp(GOBP:"wound healing")
181
+ p(HGNC:CTNNB1,var("p.Thr41Ala")) directlyIncreases act(p(HGNC:CTNNB1), ma(DEFAULT:tscript))
182
+ p(HGNC:CYCS, loc(MESHCS:Cytoplasm)) increases bp(GOBP:"apoptotic process")
183
+ p(HGNC:EDN3) causesNoChange act(p(HGNC:EDNRA))
184
+ p(HGNC:EGF) increases p(HGNC:EGFR), loc(GOCC:"cell surface"))
185
+ p(HGNC:EGF) increases p(HGNC:JAK2,pmod(Ph,Tyr))
186
+ p(HGNC:EGF) increases tloc(p(SFAM:"STAT5 Family"), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus"))
187
+ p(HGNC:EGFR,pmod(Ub,K)) directlyIncreases deg(p(HGNC:EGFR))
188
+ p(HGNC:ELANE) -> p(HGNC:MUC5AC,pmod(Glyco))
189
+ p(HGNC:ELK1,var("p.Trp379Ala")) directlyDecreases act(p(HGNC:ELK1), ma(DEFAULT:tscript))
190
+ p(HGNC:EPO) increases act(p(SFAM:"RAF Family"), ma(GO:"kinase activity"))
191
+ p(HGNC:EPO) increases p(HGNC:RAF1,pmod(Ph,Tyr,341))
192
+ p(HGNC:ERBB3) causesNoChange act(p(SFAM:"AKT Family"), ma(GO:"kinase activity"))
193
+ p(HGNC:ERBB3) causesNoChange p(SFAM:"AKT Family",pmod(MOD:PhosRes,Thr,493))
194
+ p(HGNC:EZH2) positiveCorrelation complex(p(SFAM:"Histone H3 Family",pmod(Me,Lys,27)),g(HGNC:DKK1))
195
+ p(HGNC:EZH2) positiveCorrelation complex(p(SFAM:"Histone H3 Family",pmod(Me,Lys,27)),g(HGNC:DKK1))
196
+ p(HGNC:F2) increases sec(a(CHEBI:"nitric oxide"))
197
+ p(HGNC:F2) increases sec(p(HGNC:VWF))
198
+ p(HGNC:F2) increases surf(p(HGNC:F3))
199
+ p(HGNC:F2) increases tloc(p(HGNC:SELP), fromLoc(MESHCS:"Cytoplasmic Granules"), toLoc(MESHCS:"Cell Membrane"))
200
+ p(HGNC:GP6) regulates act(p(HGNC:SYK), ma(DEFAULT:kin))
201
+ p(HGNC:GSK3A,pmod(Ph,Ser,21)) directlyDecreases act(p(HGNC:GSK3A), ma(DEFAULT:kin))
202
+ p(HGNC:HDAC4,pmod(Sumo,Lys,559)) directlyIncreases act(p(HGNC:HDAC4), ma(DEFAULT:cat))
203
+ p(HGNC:HIF1A,pmod(Ac,K,532)) directlyIncreases deg(p(HGNC:HIF1A))
204
+ p(HGNC:HIF1A,pmod(Hy,Asn,863)) directlyDecreases act(p(HGNC:HIF1A), ma(DEFAULT:tscript))
205
+ p(HGNC:HIF1A,pmod(Hy,Pro,402)) directlyIncreases complex(p(HGNC:VHL),p(HGNC:HIF1A))
206
+ p(HGNC:HIF1A,pmod(Hy,Pro,564)) directlyIncreases complex(p(HGNC:VHL),p(HGNC:HIF1A))
207
+ p(HGNC:HRAS,var(p.Gly12Val)) decreases bp(GOBP:"G1/S transition of mitotic cell cycle")
208
+ p(HGNC:HRAS,var(p.Gly12Val)) decreases sec(p(HGNC:CASP3))
209
+ p(HGNC:IGF1) directlyIncreases act(p(HGNC:IGF1R), ma(DEFAULT:kin))
210
+ p(HGNC:IGF1) regulates p(SFAM:"AKT Family",pmod(Ph,Ser,473))
211
+ p(HGNC:IKBKB,pmod(Ph)) increases act(complex(SCOMP:"Nfkb Complex"), ma(DEFAULT:tscript))
212
+ p(HGNC:IL13) increases r(HGNC:CFTR, var(r.1653_1655delcuu))
213
+ p(HGNC:IL1B) increases deg(p(HGNC:NFKBIA))
214
+ p(HGNC:IL4) increases act(p(SFAM:"PDE4 Family"), ma(GO:"catalytic activity"))
215
+ p(HGNC:IL6) increases act(p(HGNC:JAK2), ma(GO:"kinase activity"))
216
+ p(HGNC:IL6) increases act(p(HGNC:STAT3), ma(GO:"nucleic acid binding transcription factor activity"))
217
+ p(HGNC:IL6) increases act(p(HGNC:TYK2), ma(GO:"kinase activity"))
218
+ p(HGNC:IRS1,pmod(Ph,Ser)) negativeCorrelation p(HGNC:IRS1,pmod(Ph,Tyr))
219
+ p(HGNC:IRS1,pmod(Glyco,Ser)) directlyDecreases act(p(HGNC:IRS1), ma(DEFAULT:cat))
220
+ p(HGNC:IRS2,pmod(Ph,Ser)) negativeCorrelation p(HGNC:IRS2,pmod(Ph,Tyr))
221
+ p(HGNC:LRIG1) increases p(HGNC:EGFR,pmod(Ub,K))
222
+ p(HGNC:MYD88) causesNoChange r(HGNC:IFNB1)
223
+ p(HGNC:NRAS,var("p.Gln61Arg")) increases p(HGNC:RPS6KB1,pmod(Ph,Ser,447))
224
+ p(HGNC:PAWR,pmod(Ph,Thr,163)) directlyIncreases act(p(HGNC:PAWR))
225
+ p(HGNC:PLAU, frag(?)) decreases bp(GOBP:"cell migration")
226
+ p(HGNC:PLAU, frag(?, 18kD)) decreases bp(GOBP:"cell proliferation")
227
+ p(HGNC:PRKACA) increases p(HGNC:GSK3A,pmod(Ph,Ser,21))
228
+ p(HGNC:PRKACA) increases p(HGNC:GSK3B,pmod(MOD:PhosRes,Ser,9))
229
+ p(HGNC:PRPF4B,pmod(Ph)) directlyDecreases complex(p(HGNC:PRPF4B),p(HGNC:PRPF6))
230
+ p(HGNC:PRPF4B,pmod(Ph)) directlyDecreases complex(p(HGNC:PRPF4B),p(HGNC:SMARCA4))
231
+ p(HGNC:PTEN) negativeCorrelation p(SFAM:"AKT Family",pmod(Ph))
232
+ p(HGNC:PTEN) negativeCorrelation p(SFAM:"AKT Family",pmod(Ph))
233
+ p(HGNC:PTEN,var("p.Arg173Cys")) decreases p(HGNC:PTEN)
234
+ p(HGNC:RAF1,pmod(Ph,Ser,621)) directlyDecreases act(p(HGNC:RAF1), ma(GO:"kinase activity"))
235
+ p(HGNC:RAF1,pmod(Ph,Ser,621)) directlyIncreases complex(p(HGNC:RAF1),p(SFAM:"14-3-3 Family"))
236
+ p(HGNC:RAF1,pmod(Ph,Y,341)) directlyIncreases act(p(HGNC:RAF1), ma(GO:"kinase activity"))
237
+ p(HGNC:RELA,pmod(Ac,Lys,310)) increases act(complex(SCOMP:"Nfkb Complex"), ma(DEFAULT:tscript))
238
+ p(HGNC:SELE) increases p(HGNC:HSPB1,pmod(Ph))
239
+ p(HGNC:SIRT1) negativeCorrelation complex(p(SFAM:"Histone H4 Family",pmod(Ac,Lys,16)),g(HGNC:DKK1))
240
+ p(HGNC:SNRPC) causesNoChange act(p(fus(HGNC:EWSR1,?, HGNC:FLI1,?)))
241
+ p(HGNC:SUZ12) positiveCorrelation complex(p(SFAM:"Histone H3 Family",pmod(Me,Lys,27)),g(HGNC:DKK1))
242
+ p(HGNC:TGFA) directlyIncreases act(p(HGNC:EGFR), ma(GO:"kinase activity"))
243
+ p(HGNC:TGFB1) increases p(HGNC:CFTR, var("p.Thr1220Lysfs"))
244
+ p(HGNC:TGFB1) association p(HGNC:COL4A1, loc(GOCC:"extracellular matrix"))
245
+ p(HGNC:TIRAP) causesNoChange r(HGNC:IFNB1)
246
+ p(HGNC:TNF) increases act(complex(SCOMP:"Nfkb Complex"), ma(DEFAULT:tscript))
247
+ p(HGNC:TNF) directlyIncreases act(p(HGNC:TNFRSF1A))
248
+ p(HGNC:TNF) increases surf(p(HGNC:MMP14))
249
+ p(HGNC:TP53,var("p.Arg175Leu")) decreases p(HGNC:TP53)
250
+ p(HGNC:TP53,var("p.Arg181His")) directlyDecreases act(p(HGNC:TP53), ma(DEFAULT:tscript))
251
+ p(HGNC:TP53,var("p.Arg248Gln")) directlyDecreases act(p(HGNC:TP53), ma(DEFAULT:tscript))
252
+ p(HGNC:TP53,var("p.Arg273His")) increases bp(GOBP:"cell proliferation")
253
+ p(HGNC:TP53,var("p.Arg282Trp")) directlyDecreases act(p(HGNC:TP53), ma(DEFAULT:tscript))
254
+ p(HGNC:TP53,var("p.Asn239Ser")) directlyDecreases act(p(HGNC:TP53), ma(DEFAULT:tscript))
255
+ p(HGNC:TP53,var("p.Asp281Glu")) directlyDecreases act(p(HGNC:TP53), ma(DEFAULT:tscript))
256
+ p(HGNC:TP53,var("p.Pro309Ser")) directlyDecreases act(p(HGNC:TP53), ma(DEFAULT:tscript))
257
+ p(HGNC:TP63) increases composite(p(SFAM:"Histone H3 Family",pmod(Ac)),p(SFAM:"Histone H4 Family",pmod(Ac)))
258
+ p(HGNC:TP73,var("p.Arg263Trp")) directlyDecreases act(p(HGNC:TP73), ma(DEFAULT:tscript))
259
+ p(HGNC:UCP1,var("p.Met229Leu")) positiveCorrelation path(MESHD:"Diabetes Mellitus, Type 2")
260
+ p(HGNC:UCP1,var("p.Met229Leu")) positiveCorrelation path(MESHD:"Diabetes Mellitus, Type 2")
261
+ p(HGNC:VEGFA) increases p(HGNC:FLT1,pmod(Ph,Y))
262
+ p(HGNC:VEGFA) increases p(HGNC:PTK2B,pmod(Ph))
263
+ p(HGNC:VEGFA) regulates p(SFAM:"PIK3R Class IA Family",pmod(Ph,Tyr))
264
+ p(HGNC:VHL) decreases act(p(HGNC:HIF1A), ma(DEFAULT:tscript))
265
+ p(HGNC:VHL) directlyDecreases act(p(HGNC:PRKCD), ma(GO:"kinase activity"))
266
+ p(HGNC:VHL) directlyIncreases deg(p(HGNC:HIF1A))
267
+ p(HGNC:VHL) decreases surf(p(HGNC:CXCR4))
268
+ p(HGNC:VHL,var("p.Ile180Asn")) decreases p(HGNC:VHL)
269
+ p(HGNC:VTN) directlyIncreases act(complex(p(HGNC:ITGAV),p(HGNC:ITGB3)))
270
+ p(HGNC:VWF) directlyDecreases deg(p(HGNC:F8))
271
+ p(MGI:Akt1,pmod(Ph,Ser,473)) directlyIncreases p(MGI:Foxo3,pmod(Ph,Thr,32))
272
+ p(MGI:Angpt1) directlyIncreases act(p(MGI:Tek), ma(DEFAULT:kin))
273
+ p(MGI:Braf,var("p.Val600Glu") increases p(MGI:Sftpc)
274
+ p(MGI:Ctnnb1) increases act(p(MGI:Mapk1), ma(DEFAULT:kin))
275
+ p(MGI:Egf) regulates p(MGI:Akt1)
276
+ p(MGI:Hck,var("p.Tyr499Phe")) directlyIncreases act(p(MGI:Hck), ma(DEFAULT:kin))
277
+ p(MGI:Hck,var("p.Tyr499Phe")) increases p(MGI:Il5)
278
+ p(MGI:Hck,var("p.Tyr499Phe")) increases path(MESHD:Inflammation)
279
+ p(MGI:Il6st,var("p.Tyr757Phe")) directlyDecreases act(p(MGI:Il6st), ma(DEFAULT:cat))
280
+ p(MGI:Il6st,var("p.Tyr759Phe")) decreases bp(MESHPP:Apoptosis)
281
+ p(MGI:Irs1) causesNoChange p(MGI:Rps6kb2,pmod(Ph))
282
+ p(MGI:Jak3,var("p.Ala572Val")) increases p(MGI:Bcl2)
283
+ p(MGI:Kras,var("p.Gly12Asp")) increases path(MESHD:Neoplasms)
284
+ p(MGI:Mapkap1) causesNoChange p(MGI:Akt1,pmod(MOD:PhosRes,Ser,308))
285
+ p(MGI:Mapkap1) increases p(MGI:Akt1,pmod(MOD:PhosRes,Ser,473))
286
+ p(MGI:Mapkap1) increases p(MGI:Foxo3,pmod(Ph,Thr,32))
287
+ p(MGI:Pgf) directlyIncreases act(p(MGI:Flt1), ma(DEFAULT:kin))
288
+ p(MGI:Pias1) directlyDecreases act(p(MGI:Stat1), ma(GO:"nucleic acid binding transcription factor activity"))
289
+ p(MGI:Pias3) directlyDecreases act(p(HGNC:STAT3), ma(GO:"nucleic acid binding transcription factor activity"))
290
+ p(MGI:Rela,pmod(Ac,Lys,310)) directlyIncreases act(p(MGI:Rela), ma(DEFAULT:tscript))
291
+ p(MGI:Vegfb) causesNoChange bp(GOBP:"vasculature development")
292
+ p(MGI:Wnt7b) increases bp(GOBP:"lung epithelium development")
293
+ p(REF:"NP_000483.3", var("p.Phe508del")) increases act(p(SFAM:"SREBF Family"), ma(DEFAULT:tscript))
294
+ p(RGD:Chuk,pmod(MOD:PhosRes,Ser,180)) directlyIncreases act(p(RGD:Chuk), ma(DEFAULT:kin))
295
+ p(RGD:Igf1) regulates act(p(SFAM:"MAPK Erk1/2 Family"), ma(GO:"kinase activity"))
296
+ p(RGD:Igf1) increases act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp))
297
+ p(RGD:Igf1) increases act(p(SFAM:"RPS6KB Family"), ma(GO:"kinase activity"))
298
+ p(RGD:Igf1) increases p(SFAM:"RPS6KB Family",pmod(Ph,Thr,412))
299
+ p(RGD:Igf1) causesNoChange r(RGD:Myog)
300
+ p(RGD:Ikbkb,pmod(MOD:PhosRes,Ser,177)) directlyIncreases act(p(RGD:Ikbkb), ma(DEFAULT:kin))
301
+ p(RGD:Itgb4,pmod(Ph,Tyr)) directlyIncreases complex(p(RGD:Itga6),p(RGD:Itgb4),p(RGD:Shc1))
302
+ p(SFAM:"AKT Family") increases p(HGNC:IRAK1,pmod(Ph,Thr,100))
303
+ p(SFAM:"AKT Family",pmod(Ph,Ser,473)) positiveCorrelation p(SFAM:"AKT Family",pmod(MOD:PhosRes,Tyr,308))
304
+ p(SFAM:"AKT Family",pmod(Ph,Ser,473)) positiveCorrelation path(MESHD:"Carcinoma, Non-Small-Cell Lung")
305
+ p(SFAM:"AKT Family",pmod(Ph,Thr,308)) positiveCorrelation act(p(SFAM:"AKT Family"), ma(GO:"kinase activity"))
306
+ p(SFAM:"AKT Family",var("p.Lys179Met")) directlyDecreases act(p(SFAM:"AKT Family"), ma(GO:"kinase activity"))
307
+ p(SFAM:"AKT Family",var("p.Lys179Met")) increases bp(GOBP:"apoptotic process")
308
+ p(SFAM:"FOXO Family",pmod(Ac)) directlyDecreases act(p(SFAM:"FOXO Family"), , ma(GO:"nucleic acid binding transcription factor activity"))
309
+ p(SFAM:"FOXO Family",pmod(Ph)) increases tloc(p(SFAM:"FOXO Family"), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus"))
310
+ p(SFAM:"Histone H3 Family",pmod(Ac)) increases act(p(HGNC:SREBF1), ma(DEFAULT:tscript))
311
+ p(SFAM:"Histone H4 Family",pmod(Me,Arg,3)) increases act(p(HGNC:YY1), ma(DEFAULT:tscript))
312
+ p(SFAM:"IL1 Family") increases act(complex(SCOMP:"Nfkb Complex"), ma(DEFAULT:tscript))
313
+ p(SFAM:"IL1 Family") increases act(p(HGNC:IRAK1), ma(DEFAULT:kin))
314
+ p(SFAM:"IL1 Family") increases r(HGNC:SELE)
315
+ p(SFAM:"INS Family") increases p(MGI:Akt1,pmod(MOD:PhosRes,Ser,473))
316
+ p(SFAM:"IRS Family",pmod(Ph)) directlyIncreases complex(p(SFAM:"PIK3R Class IA Family"),p(SFAM:"IRS Family"))
317
+ p(SFAM:"MAPK JNK Family",pmod(Ph)) directlyIncreases act(p(SFAM:"MAPK JNK Family"), ma(GO:"kinase activity"))
318
+ p(SFAM:"PDGF Family") increases act(p(SFAM:"MAPK Erk1/2 Family"), ma(GO:"kinase activity"))
319
+ p(SFAM:"PDGF Family") increases p(MGI:Akt1,pmod(MOD:PhosRes,Ser,473))
320
+ p(SFAM:"RAS Family",pmod(Farn)) directlyIncreases act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp))
321
+ p(SFAM:"RAS Family",pmod(Farn)) directlyIncreases tloc(p(SFAM:"RAS Family"), fromLoc(MESHCS:"Intracellular Space"), toLoc(MESHCS:"Cell Membrane"))
322
+ p(SFAM:"RAS Family",pmod(Farn,L)) directlyIncreases complex(p(SFAM:"RAS Family"),p(SFAM:"RAF Family"))
323
+ p(SFAM:"VEGF Family") increases act(p(HGNC:CYBB), ma(DEFAULT:cat))
324
+ p(SFAM:"VEGF Family") directlyIncreases act(p(HGNC:KDR), ma(DEFAULT:kin))
325
+ p(SFAM:"VEGF Family") increases bp(GOBP:angiogenesis)
326
+ p(SFAM:"VEGF Family") increases complex(p(HGNC:ARF6),p(HGNC:RAC1))
327
+ p(SFAM:"VEGF Family") increases act(p(HGNC:RAC1), ma(DEFAULT:gtp))
328
+ p(SFAM:"VEGF Family") increases p(HGNC:CAV1,pmod(Ph,Y,14))
329
+ p(SFAM:"VEGF Family") directlyIncreases p(HGNC:KDR,pmod(Ph,Y,1054))
330
+ path(SDIS:"Type II diabetes") negativeCorrelation act(p(HGNC:ATP5B), ma(DEFAULT:cat))
331
+ path(SDIS:"Type II diabetes") negativeCorrelation act(p(HGNC:SLC2A4), ma(DEFAULT:tport))
332
+ path(SDIS:"Type II diabetes") negativeCorrelation tloc(p(HGNC:SLC2A4), fromLoc(GOCC:"cytoplasmic, membrane-bounded vesicle"), toLoc(GOCC:"cell outer membrane))
333
+ path(SDIS:Diabetes) negativeCorrelation act(complex(SCOMP:"p85/p110 PI3Kinase Complex"), ma(GO:"kinase activity"))
334
+ r(fus(HGNC:TMPRSS2, "r.1_79", HGNC:ERG, "r.312_5034")) association path(SDIS:"prostate cancer")
335
+ rxn(reactants(a(CHEBI:"acetyl-CoA")),products(a(SCHEM:Citrate))) subProcessOf bp(GOBP:"tricarboxylic acid cycle")
336
+ rxn(reactants(a(CHEBI:glucose)),products(a(CHEBI:pyruvate))) subProcessOf bp(MESHPP:Glycolysis)
337
+ tloc(p(HGNC:AIFM1), fromLoc(MESHCS:Mitochondria), toLoc(MESHCS:Cytoplasm)) increases bp(GOBP:"apoptotic DNA fragmentation")
338
+ tloc(p(HGNC:CTNNB1), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus")) increases complex(p(HGNC:CTNNB1),p(HGNC:BCL9))
339
+ tloc(p(HGNC:CYCS), fromLoc(MESHCS:Mitochondria), toLoc(MESHCS:Cytoplasm)) increases bp(GOBP:"apoptotic process")
340
+ tloc(p(HGNC:HDAC4), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus")) directlyIncreases p(HGNC:HDAC4,pmod(Sumo,Lys,559))
341
+ tloc(p(HGNC:PAWR), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus")) decreases act(complex(SCOMP:"Nfkb Complex"), ma(DEFAULT:tscript))
342
+ tloc(p(HGNC:SGK1),fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus")) association bp(GOBP:"cell cycle")
343
+ tloc(p(SFAM:"DVL Family"), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Membrane")) increases complex(p(SFAM:"DVL Family"),p(SFAM:"DVL Family"))
344
+ tloc(p(SFAM:"FOXO Family"), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus")) increases act(p(SFAM:"FOXO Family"), ma(GO:"nucleic acid binding transcription factor activity"))
data/bin/bel2_document_examples.bel ADDED
@@ -0,0 +1,250 @@
1
+ complex(p(HGNC:CCND1), p(HGNC:CDK4))
2
+ p(HGNC:CCND1) => act(p(HGNC:CDK4))
3
+ p(HGNC:BCL2)-| bp(MESHPP:Apoptosis)
4
+ p(HGNC:GATA1) => ( act(p(HGNC:ZBTB16)) => r(HGNC:MPL) )
5
+ a(CHEBI:"oxygen atom")
6
+ a(CHEBI:thapsigargin)
7
+ complex(SCOMP:"AP-1 Complex")
8
+ complex(p(HGNC:FOS), p(HGNC:JUN))
9
+ composite(p(HGNC:IL6), complex(GOCC:"interleukin-23 complex")) increases bp(GOBP:"T-helper 17 cell differentiation")
10
+ complex(p(HGNC:TP53), g(HGNC:CDKN1A))
11
+ m(HGNC:MIR21)
12
+ p(HGNC:AKT1)
13
+ p(SFAM:"AKT Family")
14
+ r(HGNC:AKT1)
15
+ p(ns:protein_value, pmod(ns:type_value, <code>, <pos>))
16
+ p(HGNC:AKT1, pmod(Ph, S, 473))
17
+ p(HGNC:AKT1, pmod(Ph, Ser, 473))
18
+ p(HGNC:AKT1, pmod(MOD:PhosRes, Ser, 473))
19
+ p(HGNC:MAPK1, pmod(Ph, Thr, 185), pmod(Ph, Tyr, 187))
20
+ p(HGNC:HRAS, pmod(Palm))
21
+ p(HGNC:CFTR, var("="))
22
+ p(HGNC:CFTR, var("?"))
23
+ p(HGNC:CFTR, var("p.Gly576Ala"))
24
+ p(REF:NP_000483.3, var("p.Gly576Ala"))
25
+ p(HGNC:CFTR, var("p.Phe508del"))
26
+ p(REF:NP_000483.3, var("p.Phe508del"))
27
+ p(HGNC:CFTR, var("p.Thr1220Lysfs"))
28
+ p(REF:NP_000483.3, var("p.Thr1220Lysfs"))
29
+ g(SNP:rs113993960, var("delCTT"))
30
+ g(REF:NC_000007.13, var("g.117199646_117199648delCTT"))
31
+ g(HGNC:CFTR, var("c.1521_1523delCTT"))
32
+ g(REF:NM_000492.3, var("c.1521_1523delCTT"))
33
+ r(HGNC:CFTR, var("c.1521_1523delCTT"))
34
+ r(REF:NM_000492.3, var("c.1521_1523delCTT"))
35
+ r(HGNC:CFTR, var("r.1653_1655delcuu"))
36
+ r(REF:NM_000492.3, var("r.1653_1655delcuu"))
37
+ p(HGNC:YFG, frag(5_20))
38
+ p(HGNC:YFG, frag(1_?))
39
+ p(HGNC:YFG, frag(?_*))
40
+ p(HGNC:YFG, frag(?))
41
+ p(HGNC:YFG, frag(?, 55kD))
42
+ p(HGNC:AKT1, loc(MESHCS:Cytoplasm))
43
+ a(CHEBI:"calcium(2+)", loc(GOCC:"endoplasmic reticulum"))
44
+ bp(GOBP:"cell cycle arrest")
45
+ bp(GOBP:angiogenesis)
46
+ pathology(MESHD:"Pulmonary Disease, Chronic Obstructive")
47
+ pathology(MESHD:adenocarcinoma)
48
+ act(p(HGNC:AKT1))
49
+ act(p(HGNC:FOXO1), ma(DEFAULT:tscript))
50
+ act(p(HGNC:FOXO1), ma(GO:"nucleic acid binding transcription factor activity"))
51
+ act(p(HGNC:AKT1), ma(DEFAULT:kin))
52
+ act(p(HGNC:AKT1), ma(GO:"kinase activity"))
53
+ tloc(p(HGNC:EGFR), fromLoc(GOCC:"cell surface"), toLoc(GOCC:endosome))
54
+ tloc(<abundance>, fromLoc(GOCC:intracellular), toLoc(GOCC:"extracellular space"))
55
+ tloc(<abundance>, fromLoc(GOCC:intracellular), toLoc(GOCC:"cell surface"))
56
+ deg(<abundance>) directlyDecreases <abundance>
57
+ rxn(reactants(a(CHEBI:superoxide)),products(a(CHEBI:"hydrogen peroxide"), a(CHEBI: "oxygen"))
58
+ fus(ns5':v5', "range5'", ns3':v3', "range3'")
59
+ r(fus(HGNC:TMPRSS2, "r.1_79", HGNC:ERG, "r.312_5034"))
60
+ r(fus(HGNC:TMPRSS2, "?", HGNC:ERG, "?"))
61
+ act(p(HGNC:HMGCR), ma(DEFAULT:cat)) rateLimitingStepOf bp(GOBP:"cholesterol biosynthetic process")
62
+ p(PFH:"Hedgehog Family") =| act(p(HGNC:PTCH1))
63
+ act(p(HGNC:FOXO3),ma(DEFAULT:tscript)) =| r(HGNC:MIR21)
64
+ p(HGNC:CLSPN) => (act(p(HGNC:ATR), ma(DEFAULT:kin)) => p(HGNC:CHEK1, pmod(P)))
65
+ p(HGNC:GSK3B, pmod(P, S, 9)) =| act(p(HGNC:GSK3B), ma(DEFAULT:kin))
66
+ g(HGNC:AKT1) orthologous g(MGI:AKT1)
67
+ g(HGNC:AKT1) :> r(HGNC:AKT1)
68
+ r(HGNC:AKT1) >> p(HGNC:AKT1)
69
+ pathology(MESH:Psoriasis) isA pathology(MESH:"Skin Diseases")
70
+ abundance(CHEBI:"nitrogen atom")
71
+ abundance(CHEBI:"prostaglandin J2")
72
+ a(CHEBI:"nitrogen atom")
73
+ a(CHEBI:"prostaglandin J2")
74
+ geneAbundance(HGNC:AKT1)
75
+ rnaAbundance(HGNC:AKT1)
76
+ proteinAbundance(HGNC:AKT1)
77
+ g(HGNC:AKT1)
78
+ r(HGNC:AKT1)
79
+ p(HGNC:AKT1)
80
+ r(EGID:207)
81
+ r(SP:P31749)
82
+ p(SFAM:"AKT Family")
83
+ geneAbundance(MGI:Mir21)
84
+ rnaAbundance(MGI:Mir21)
85
+ microRNAAbundance(MGI:Mir21)
86
+ g(MGI:Mir21)
87
+ r(MGI:Mir21)
88
+ m(MGI:Mir21)
89
+ complexAbundance(GOCC:"IkappaB kinase complex")
90
+ complexAbundance(proteinAbundance(HGNC:CHUK), proteinAbundance(HGNC:IKBKB), proteinAbundance(HGNC:IKBKG))
91
+ complex(GOCC:"IkappaB kinase complex")
92
+ complex(p(HGNC:CHUK), p(HGNC:IKBKB), p(HGNC:IKBKG))
93
+ compositeAbundance(proteinAbundance(HGNC:TGFB1), proteinAbundance(HGNC:IL6))
94
+ composite(p(HGNC:TGFB1), p(HGNC:IL6))
95
+ activity(proteinAbundance(HGNC:TLR7))
96
+ act(p(HGNC:TLR7))
97
+ activity(proteinAbundance(RGD:Sod1), ma(DEFAULT:cat))
98
+ activity(proteinAbundance(RGD:Sod1), molecularActivity(GOMF:"catalytic activity"))
99
+ act(p(RGD:Sod1), ma(DEFAULT:cat))
100
+ act(p(RGD:Sod1), ma(GOMF:"catalytic activity"))
101
+ activity(proteinAbundance(MGI:Casp3), molecularActivity(DEFAULT:pep))
102
+ activity(proteinAbundance(MGI:Casp3), molecularActivity(GOMF:"peptidase activity"))
103
+ act(p(MGI:Casp3), ma(DEFAULT:pep))
104
+ act(p(MGI:Casp3), ma(GOMF:"peptidase activity"))
105
+ activity(proteinAbundance(SFAM:"RAS Family"), molecularActivity(DEFAULT:gtp))
106
+ activity(proteinAbundance(SFAM:"RAS Family"), molecularActivity(GOMF:"GTP binding"))
107
+ act(p(SFAM:"RAS Family"), ma(DEFAULT:gtp))
108
+ act(p(SFAM:"RAS Family"), ma(GOMF:"GTP binding"))
109
+ activity(complexAbundance(SCOMP:"ENaC Complex"), molecularActivity(DEFAULT:tport))
110
+ activity(complexAbundance(SCOMP:"ENaC Complex"), molecularActivity(GOMF:"transporter activity"))
111
+ act(complex(NCH:"ENaC Complex"), ma(DEFAULT:tport))
112
+ act(complex(NCH:"ENaC Complex"), ma(GOMF:"transporter activity"))
113
+ activity(proteinAbundance(HGNC:CANX), molecularActivity(DEFAULT:chap))
114
+ act(p(HGNC:CANX), ma(DEFAULT:chap))
115
+ activity(proteinAbundance(MGI:Trp53), molecularActivity(DEFAULT:tscript))
116
+ activity(proteinAbundance(MGI:Trp53), molecularActivity(GOMF:"nucleic acid binding transcription factor activity"))
117
+ act(p(MGI:Trp53), ma(DEFAULT:tscript))
118
+ act(p(MGI:Trp53), ma(GOMF:"nucleic acid binding transcription factor activity"))
119
+ complexAbundance(proteinAbundance(HGNC:AKT1S1), proteinAbundance(HGNC:MTOR))
120
+ complex(p(HGNC:AKT1S1), p(HGNC:MTOR))
121
+ FKBP12/rapamycin-associated protein (FRAP), mammalian target of
122
+ rapamycin (mTOR), associates with Stat3 and facilitates STAT activation."
123
+ proteinAbundance(HGNC:BMP4) increases complexAbundance(proteinAbundance(HGNC:MTOR), proteinAbundance(HGNC:STAT3))
124
+ p(HGNC:BMP4) -> complex(p(HGNC:MTOR), p(HGNC:STAT3))
125
+ proteinAbundance(HGNC:IL17A) increases complexAbundance(proteinAbundance(HGNC:STAT3), geneAbundance(HGNC:CCL11))
126
+ p(HGNC:IL17A) -> complex(p(HGNC:STAT3), g(HGNC:CCL11))
127
+ complexAbundance(abundance(CHEBI:"1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate"), proteinAbundance(HGNC:AKT1))
128
+ complex(a(CHEBI:"1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate"), p(HGNC:AKT1))
129
+ biologicalProcess(GOBP:"cellular senescence")
130
+ bp(GOBP:"cellular senescence")
131
+ pathology(MESHD:"Muscle Hypotonia")
132
+ path(MESHD:"Muscle Hypotonia")
133
+ proteinAbundance(HGNC:HIF1A, proteinModification(Hy, Asn, 803))
134
+ p(HGNC:HIF1A, pmod(Hy, N, 803))
135
+ p(SFAM:"AKT Family", pmod(Ph))
136
+ p(MGI:Rela, pmod(Ac, Lys, 315))
137
+ p(HGNC:SP1, pmod(Glyco))
138
+ p(RGD:STAT1, pmod(Me, Arg))
139
+ p(HGNC:MYC, pmod(Ub, Lys))
140
+ reaction(reactants(abundance(CHEBI:phosphoenolpyruvate), abundance(CHEBI:ADP)), products(abundance(CHEBI:pyruvate), abundance(CHEBI:ATP)))
141
+ rxn(reactants(a(CHEBI:phophoenolpyruvate), a(CHEBI:ADP)), products(a(CHEBI:pyruvate), a(CHEBI:ATP)))
142
+ translocation(proteinAbundance(HGNC:NFE2L2), fromLoc(MESHCS:Cytoplasm), toLoc(MESHCS:"Cell Nucleus"))
143
+ tloc(p(HGNC:NFE2L2), fromLoc(MESHCL:Cytoplasm), toLoc(MESHCL:"Cell Nucleus"))
144
+ cellSecretion(proteinAbundance(MGI:Il6))
145
+ sec(p(MGI:Il6))
146
+ cellSurfaceExpression(proteinAbudance(RGD:Fas))
147
+ surf(p(RGD:Fas))
148
+ degradation(rnaAbundance(HGNC:MYC))
149
+ deg(r(HGNC:MYC))
150
+ proteinAbundance(HGNC:PIK3CA, variant("p.Glu545Lys"))
151
+ p(HGNC:PIK3CA, var("p.Glu545Lys"))
152
+ proteinAbundance(HGNC:ABCA1, variant("p.Arg1851*"))
153
+ p(HGNC:ABCA1, var("p.Arg1851*"))
154
+ proteinAbundance(fusion(HGNC:BCR, "p.1_426", HGNC:JAK2, "p.812_1132"))
155
+ p(fus(HGNC:BCR, "p.1_426", HGNC:JAK2, "p.812_1132"))
156
+ p(fus(HGNC:BCR, "?", HGNC:JAK2, "?"))
157
+ proteinAbundance(HGNC:IL6) increases rnaAbundance(HGNC:ENO1)
158
+ proteinAbundance(HGNC:IL6) increases rnaAbundance(HGNC:XBP1)
159
+ p(HGNC:IL6) -> r(HGNC:ENO1)
160
+ p(HGNC:IL6) -> r(HGNC:XBP1)
161
+ abundance(CHEBI:corticosteroid) decreases biologicalProcess(MESHD:Inflammation)
162
+ a(CHEBI:corticosteroid) -| path(MESHD:Inflammation)
163
+ proteinAbundance(HGNC:AREG) increases activity(complexAbundance(GOCC:"NF-kappaB complex"), molecularActivity(DEFAULT:tscript))
164
+ proteinAbundance(HGNC:EGF) causesNoChange activity(complexAbundance(GOCC:"NF-kappaB complex"), molecularActivity(DEFAULT:tscript))
165
+ p(HGNC:AREG) -> act(complex(GOCC:"NF-kappaB complex"), ma(DEFAULT:tscript))
166
+ p(HGNC:EGF) causesNoChange act(complex(GOCC:"NF-kappaB complex"), ma(DEFAULT:tscript))
167
+ proteinAbundance(HGNC:FGF2, location(GOCC:cytoplasm)) positiveCorrelation pathology(MESHD:"Pulmonary Disease, Chronic Obstructive")
168
+ proteinAbundance(MGI:Nr2f2) association biologicalProcess(GOBP:angiogenesis)
169
+ p(MGI:NR2F2) -- bp(GOBP:angiogenesis)
170
+ proteinAbundance(HGNC:AREG) directlyIncreases activity(proteinAbundance(HGNC:EGFR), molecularActivity(DEFAULT:kin))
171
+ p(HGNC:AREG) => act(p(HGNC:EGFR), ma(DEFAULT:kin))
172
+ activity(proteinAbundance(HGNC:CDK1), molecularActivity(DEFAULT:kin)) directlyIncreases proteinAbundance(HGNC:FOXO1, proteinModification(Ph, Ser, 249))
173
+ act(p(HGNC:CDK1), ma(DEFAULT:kin)) => p(HGNC:FOXO1, pmod(Ph, S, 249))
174
+ activity(proteinAbundance(HGNC:ALOX5), molecularActivity(DEFAULT:cat)) directlyIncreases reaction(reactants(abundance(CHEBI:"5(S)-HPETE")), products(abundance(CHEBI:"leukotriene A4"), abundance(CHEBI:water)))
175
+ act(p(HGNC:ALOX5), ma(DEFAULT:cat)) => rxn(reactants(a(CHEBI:"5(S)-HPETE")), products(a(CHEBI:"leukotriene A4"), a(CHEBI:water)))
176
+ proteinAbundance(HGNC:GSK3A, proteinModification(Ph, Ser, 21)) directlyDecreases activity(proteinAbundance(HGNC:GSK3A))
177
+ proteinAbundance(HGNC:GSK3B, proteinModification(Ph, Ser, 9)) directlyDecreases activity(proteinAbundance(HGNC:GSK3B))
178
+ p(HGNC:GSK3A, pmod(Ph, S, 21)) =| act(p(HGNC:GSK3A))
179
+ p(HGNC:GSK3B, pmod(Ph, S, 9)) =| act(p(HGNC:GSK3B))
180
+ activity(proteinAbundance(HGNC:FOXO1), molecularActivity(DEFAULT:tscript)) directlyIncreases rnaAbundance(HGNC:CEBPB)
181
+ act(p(HGNC:FOXO1), ma(DEFAULT:tscript)) => r(HGNC:CEBPB)
182
+ proteinAbundance(HGNC:CLSPN) increases (activity(proteinAbundance(HGNC:ATR), molecularActivity(DEFAULT:kin)) directlyIncreases proteinAbundance(HGNC:CHEK1, proteinModification(Ph)))
183
+ p(HGNC:CLSPN) -> (act(p(HGNC:ATR), ma(DEFAULT:kin)) => p(HGNC:CHEK1, pmod(Ph)))
184
+ p(SFAM:"MAPK JNK Family") hasMembers list(p(HGNC:MAPK8), p(HGNC:MAPK9))
185
+ p(SFAM:"MAPK JNK Family") hasMember p(HGNC:MAPK8)
186
+ p(SFAM:"MAPK JNK Family") hasMember p(HGNC:MAPK9)
187
+ complex(GOCC:"checkpoint clamp complex") hasComponents list(p(HGNC:RAD9A), p(HGNC:RAD1), p(HGNC:HUS1))
188
+ complex(GOCC:"checkpoint clamp complex") hasComponent p(HGNC:RAD9A)
189
+ complex(GOCC:"checkpoint clamp complex") hasComponent p(HGNC:RAD1)
190
+ complex(GOCC:"checkpoint clamp complex") hasComponent p(HGNC:HUS1)
191
+ a(SCHEM:"LY 294002") -| r(HGNC:TGFB2)
192
+ act(p(HGNC:PIK3CA), ma(DEFAULT:kin)) -> r(HGNC:TGFB2)
193
+ p(HGNC:FOXO1, var("p.Ser256Ala")) =| p(HGNC:FOXO1, pmod(Ph, Ser, 256))
194
+ p(HGNC:FOXO1, var("p.Ser256Ala")) =| (p(SFAM:"AKT Family") => p(HGNC:FOXO1, pmod(Ph, Thr, 24)))
195
+ p(HGNC:FOXO1, var("p.Ser256Ala")) =| (p(SFAM:"AKT Family") => p(HGNC:FOXO1, pmod(Ph, Ser, 319)))
196
+ p(HGNC:FOXO1, pmod(Ph, Ser, 256)) =>(p(SFAM:"AKT Family") => p(HGNC:FOXO1, pmod(Ph, Thr, 24)))
197
+ p(HGNC:FOXO1, pmod(Ph, Ser, 256)) =>(p(SFAM:"AKT Family") => p(HGNC:FOXO1, pmod(Ph, Ser, 319)))
198
+ composite(p(MGI:Tgfb1), p(MGI:Il6)) -> bp(GOBP:"T-helper 17 cell differentiation")
199
+ composite(p(MGI:Hgf), p(MGI:Met)) -> r(MGI:Itgav)
200
+ kin(p(MGI:Met) ) -> r(MGI:Itgav)
201
+ p(MGI:Hgf) -> r(MGI:Itgav)
202
+ p(MGI:Nfe2l2) -> r(MGI:Gsta1)
203
+ p(HGNC:PTEN) -| p(HGNC:CDKN1A)
204
+ p(HGNC:SIAH2) => deg(p(HGNC:TPX2))
205
+ p(MGI:Tert) -> bp(GOBP:"cell proliferation")
206
+ act(p(MGI:Tert), ma(DEFAULT:cat)) causesNoChange bp(GOBP:"cell proliferation")
207
+ p(HGNC:RIPK1) -> act(p(GOCC:"NF-kappaB complex"), ma(DEFAULT:tscript))
208
+ act(p(HGNC:RIPK1), ma(DEFAULT:kin)) causesNoChange act(p(GOCC:"NF-kappaB complex"), ma(DEFAULT:tscript))
209
+ act(p(MGI:Met), ma(DEFAULT:kin)) -> r(Mgi:Itgav)
210
+ act(p(MGI:Met), ma(DEFAULT:kin)) -> r(Mgi:Itga3)
211
+ act(p(MGI:Met), ma(DEFAULT:kin)) -> r(Mgi:Itgb1)
212
+ p(MGI:Ctnnb1) -> r(MGI:Hhip)
213
+ p(HGNC:EGFR, var("p.Leu858Arg")) negativeCorrelation p(HGNC:ERBB2, pmod(Ph,Tyr,1248))
214
+ p(HGNC:EGFR, var("p.Leu858Arg")) -> r(HGNC:DUSP6)
215
+ p(HGNC:PAWR) -| p(SFAM:"AKT Family", pmod(Ph, Ser, 473))
216
+ p(HGNC:PAWR) -| p(SFAM:"AKT Family", pmod(Ph, Ser, 473))
217
+ p(HGNC:PAWR) -| p(SFAM:"AKT Family", pmod(Ph, Ser, 473))
218
+ p(HGNC:AKT1, pmod(Ph, Ser, 473))
219
+ p(HGNC:AKT1, pmod(Ph, Ser))
220
+ p(HGNC:AKT1, pmod(Ph))
221
+ act(p(SFAM:"AKT Family"), ma(DEFAULT:kin)) => (act(p(HGNC:SKP2)) => deg(p(SFAM:"FOXO Family")))
222
+ p(SFAM:"FOXO Family", pmod(Ph)) => (act(p(HGNC:SKP2)) => deg(p(SFAM:"FOXO Family")))
223
+ p(HGNC:HIF1A, pmod(Hy, Pro, 402)) => complex(p(HGNC:HIF1A), p(HGNC:VHL))
224
+ p(HGNC:HIF1A, pmod(Hy, Pro, 564)) => complex(p(HGNC:HIF1A), p(HGNC:VHL))
225
+ complex(p(HGNC:HIF1A, pmod(Hy, Pro, 402)), p(HGNC:VHL))
226
+ a(SCHEM:"smoke condensate, cigarette (gas phase)") -> complex(p(PFH:"Histone H3 Family",pmod(Me3, Lys, 27)), g(HGNC:DKK1))
227
+ p(HGNC:MAPK3, pmod(Ph, Thr, 202)) => act(p(HGNC:MAPK3), ma(DEFAULT:kin))
228
+ p(HGNC:MAPK3, pmod(Ph, Tyr, 204)) => act(p(HGNC:MAPK3), ma(DEFAULT:kin))
229
+ p(HGNC:MAPK3, pmod(Ph, Thr, 202)), pmod(Ph, Tyr, 204)) => act(p(HGNC:MAPK3), ma(DEFAULT:kin))
230
+ p(HGNC:CTNNB1, pmod(Ph, Ser, 45)) => p(HGNC:CTNNB1, pmod(Ph, Thr, 41))
231
+ p(HGNC:CTNNB1, pmod(Ph, Ser, 45)) => (kin(p(SFAM:"GSK3 Family")) => p(HGNC:CTNNB1, pmod(Ph, Thr, 41)))
232
+ act(p(HGNC:STAMBP)) =| p(HGNC:F2RL1, pmod(Ub))
233
+ act(p(HGNC:CDC25C), ma(DEFAULT:phos)) =| p(HGNC:CDK1, pmod(Ph, Tyr, 15))
234
+ act(p(HGNC:HSD11B1), ma(DEFAULT:cat)) => rxn(reactants(a(CHEBI:NADPH), a(CHEBI:cortisone)), products(a(CHEBI:"NADP(+)"), a(CHEBI:cortisol)))
235
+ act(p(HGNC:HSD11B1), ma(DEFAULT:cat)) => rxn(reactants(a(CHEBI:"NADP(+)"), a(CHEBI:cortisol)), products(a(CHEBI:NADPH), a(CHEBI:cortisone)))
236
+ act(p(HGNC:SOD1), ma(DEFAULT:cat)) => rxn(reactants(a(CHEBI:superoxide)), products(a(CHEBI:"hydrogen peroxide")))
237
+ act(p(HGNC:SOD1), ma(DEFAULT:cat)) =| a(CHEBI:superoxide)
238
+ act(p(HGNC:SOD1), ma(DEFAULT:cat)) => a(CHEBI:"hydrogen peroxide")
239
+ complex(p(MGI:EPOR), p(MGI:CSF2RB))
240
+ complex(p(HGNC:KEAP1), a(CHEBI:"15-deoxy-Delta(12,14)-prostaglandin J2"))
241
+ complex(p(HGNC:KEAP1), p(HGNC:RBX1), p(HGNC:CUL3))
242
+ complex(p(GOCC:"AP1 complex"), g(HGNC:CCL23))
243
+ act(p(SFAM:"AKT Family"), ma(DEFAULT:kin)) => p(HGNC:MDM2, pmod(Ph,Ser,166))
244
+ act(p(SFAM:"AKT Family"), ma(DEFAULT:kin)) => p(HGNC:MDM2, pmod(Ph,Ser,186))
245
+ act(p(PFH:"MAPK p38 Family"), ma(DEFAULT:kin)) => p(HGNC:SIAH2, pmod(Ph, Thr, 24))
246
+ act(p(PFH:"MAPK p38 Family"), ma(DEFAULT:kin)) => p(HGNC:SIAH2, pmod(Ph, Ser, 29))
247
+ complex(p(SFAM:"Hedgehog Family"), p(MGI:Hhip))
248
+ complex(p(MGI:Ihh), p(MGI:Hhip))
249
+ complex(p(MGI:Shh), p(MGI:Hhip))
250
+ complex(p(MGI:Dhh), p(MGI:Hhip))