*avis*
~~~~~~~~~~~~~~~~
################
*nodetypedef*
~~~~~~~~~~~~~~~~
id:default
color:plum3
type:\AVIS_compartment\
url:http://au.expasy.org/cgi-bin/niceprot.pl?\AVIS_humanswissprot\
xscale:2
----------------
id:Cytosol
color:yellow
----------------
id:ER
color:orange
----------------
id:Extracellular
color:tan
----------------
id:Membrane
color:coral1
----------------
id:Mitochondria
color:turquoise
----------------
----------------
id:Nucleus
color:DeepSkyBlue
----------------
id:Ribosomes
color:purple1
----------------
id:Vesicles
color:DarkOliveGreen1
----------------
################
*edgetypedef*
~~~~~~~~~~~~~~~~
id:default
reference:\AVIS_pmid\
type:\AVIS_effect\
url:http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=\AVIS_reference\
headsize:0.5
----------------
id:+
color:darkgreen
head:arrow
----------------
id:0
color:blue
head:ball
tail:ball
----------------
----------------
id:_
color:red
head:tee
----------------
id:t
color:black
head:arrow
----------------
################
*nodes*
~~~~~~~~~~~~~~~~
id:default
----------------
id:AA
compartment:Cytosol
role:Lipid
x:61.4285714285714
y:61.6666666666667
----------------
id:CALCIUM
compartment:Cytosol
role:Messenger
x:78.5714285714286
y:50.3333333333333
----------------
id:DAG
compartment:Cytosol
role:Lipid
x:67.1428571428571
y:27.6666666666667
----------------
id:EGFR
compartment:Membrane
humanswissprot:P00533
mouseswissprot:Q01279
role:Receptor
x:44.2857142857143
y:5
----------------
id:GRB2
compartment:Cytosol
humanswissprot:P62993
mouseswissprot:Q60631
role:Adapter
x:32.8571428571429
y:16.3333333333333
----------------
id:IP3
compartment:Cytosol
role:Lipid
x:90
y:27.6666666666667
----------------
id:ITPR1
compartment:ER
humanswissprot:Q14643
mouseswissprot:P11881
role:Channel
x:90
y:39
----------------
id:MAP4K1
compartment:Cytosol
humanswissprot:Q92918
mouseswissprot:P70218
role:Kinase
x:21.4285714285714
y:61.6666666666667
----------------
id:MAPK1
compartment:Cytosol
humanswissprot:P28482
mouseswissprot:P63085
role:Kinase
x:27.1428571428571
y:73
----------------
----------------
id:NRAS
compartment:Cytosol
humanswissprot:P01111
mouseswissprot:P08556
role:GTPase
x:10
y:39
----------------
id:Nucleus
scale:3
type:Nucleus
x:44.2857142857143
y:90
----------------
id:PLAA
compartment:Cytosol
humanswissprot:Q9Y263
mouseswissprot:P27612
role:Phospholipase
x:44.2857142857143
y:73
----------------
id:PLCG1
compartment:Cytosol
humanswissprot:P19174
mouseswissprot:Q62077
role:Phospholipase
x:72.8571428571429
y:16.3333333333333
----------------
id:PRKCA
compartment:Cytosol
humanswissprot:P17252
mouseswissprot:P20444
role:Kinase
x:44.2857142857143
y:50.3333333333333
----------------
id:RAF1
compartment:Cytosol
humanswissprot:P04049
mouseswissprot:Q99N57
role:Kinase
x:15.7142857142857
y:50.3333333333333
----------------
id:RASGRP3
compartment:Cytosol
humanswissprot:Q8IV61
role:GEF
x:67.1428571428571
y:39
----------------
id:SHC1
compartment:Cytosol
humanswissprot:P29353
mouseswissprot:P98083
role:Adapter
x:15.7142857142857
y:16.3333333333333
----------------
id:SOS1
compartment:Cytosol
humanswissprot:Q07889
mouseswissprot:Q62245
role:GEF
x:23.7142857142857
y:27.6666666666667
----------------
################
*edges*
~~~~~~~~~~~~~~~~
id:default
----------------
id:AA->PRKCA [+]
effect:+
pmid:2119631
pmid:3934001
reaction:Binding
source:AA
target:PRKCA
----------------
id:CALCIUM->PRKCA [+]
effect:+
pmid:438153
reaction:Binding
source:CALCIUM
target:PRKCA
----------------
id:CALCIUM->RASGRP3 [+]
effect:+
pmid:9582122
reaction:Binding
source:CALCIUM
target:RASGRP3
----------------
id:DAG->PRKCA [+]
effect:+
pmid:438153
reaction:Binding
source:DAG
target:PRKCA
----------------
id:DAG->RASGRP3 [+]
effect:+
pmid:9582122
reaction:Binding
source:DAG
target:RASGRP3
----------------
id:EGFR->GRB2 [+]
effect:+
pmid:1322798
reaction:Binding
source:EGFR
target:GRB2
----------------
id:EGFR->PLCG1 [+]
effect:+
pmid:2472219
reaction:Phosphorylation
source:EGFR
target:PLCG1
----------------
id:EGFR->SHC1 [+]
effect:+
pmid:8808684
pmid:7681824
reaction:Binding
source:EGFR
target:SHC1
----------------
id:GRB2->SOS1 [+]
effect:+
pmid:8479540
pmid:8493579
reaction:Binding
source:GRB2
target:SOS1
----------------
id:IP3->ITPR1 [+]
effect:+
pmid:2826483
pmid:3027583
pmid:1374893
pmid:2847175
reaction:Binding
source:IP3
target:ITPR1
----------------
id:ITPR1->CALCIUM [+]
effect:+
pmid:3027583
pmid:2847175
reaction:Opening
source:ITPR1
target:CALCIUM
----------------
id:MAP4K1->MAPK1 [+]
effect:+
pmid:8226933
pmid:1381507
reaction:Phosphorylation
source:MAP4K1
target:MAPK1
----------------
id:MAPK1->Nucleus
source:MAPK1
target:Nucleus
type:t
----------------
id:MAPK1->PLAA [+]
effect:+
pmid:8381049
reaction:Phosphorylation
source:MAPK1
target:PLAA
----------------
id:NRAS->RAF1 [+]
effect:+
pmid:9001246
pmid:9867809
pmid:7811320
pmid:8636091
reaction:Binding
source:NRAS
target:RAF1
----------------
id:PLAA->AA [+]
effect:+
pmid:2119631
pmid:874074
reaction:Synthesis
source:PLAA
target:AA
----------------
id:PLCG1->DAG [+]
effect:+
pmid:2831461
reaction:Synthesis
source:PLCG1
target:DAG
----------------
id:PLCG1->IP3 [+]
effect:+
pmid:2831461
pmid:3040753
pmid:2840660
pmid:3541924
reaction:Synthesis
source:PLCG1
target:IP3
----------------
id:PRKCA->EGFR [_]
effect:_
pmid:6321473
reaction:Phosphorylation
source:PRKCA
target:EGFR
----------------
id:PRKCA->PLAA [+]
effect:+
pmid:12423237
reaction:Phosphorylation
source:PRKCA
target:PLAA
----------------
id:PRKCA->RAF1 [+]
effect:+
pmid:7935389
pmid:9447975
pmid:1437148
reaction:Phosphorylation
source:PRKCA
target:RAF1
----------------
id:PRKCA->RASGRP3 [+]
effect:+
pmid:12730099
pmid:15213298
reaction:Phosphorylation
source:PRKCA
target:RASGRP3
----------------
id:RAF1->MAP4K1 [+]
effect:+
pmid:7624324
reaction:Phosphorylation
source:RAF1
target:MAP4K1
----------------
id:RASGRP3->NRAS [+]
effect:+
pmid:2833817
pmid:10934204
pmid:9582122
reaction:GEF
source:RASGRP3
target:NRAS
----------------
id:SHC1--GRB2 [0]
effect:0
pmid:8808684
pmid:8491186
pmid:8114695
pmid:9566877
pmid:1465135
reaction:Binding
source:SHC1
target:GRB2
----------------
id:SHC1->SOS1 [+]
effect:+
pmid:8114695
reaction:Binding
source:SHC1
target:SOS1
----------------
id:SOS1->NRAS [+]
effect:+
pmid:9690470
pmid:7923364
pmid:8493579
reaction:GEF
source:SOS1
target:NRAS
----------------
################