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BIOMD0000000146 - Hatakeyama2003_MAPK

 

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Reference Publication
Publication ID: 12691603
Hatakeyama M, Kimura S, Naka T, Kawasaki T, Yumoto N, Ichikawa M, Kim JH, Saito K, Saeki M, Shirouzu M, Yokoyama S, Konagaya A.
A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling.
Biochem. J. 2003 Jul; 373(Pt 2): 451-463
RIKEN Genomic Sciences Center, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. marikoh@gsc.riken.go.jp  [more]
Model
Original Model: BIOMD0000000146.origin
Submitter: Enuo He
Submission ID: MODEL8256371999
Submission Date: 06 Sep 2007 08:06:00 UTC
Last Modification Date: 26 May 2014 23:17:39 UTC
Creation Date: 16 Jul 2008 13:00:01 UTC
Encoders:  Enuo He
   Lukas Endler
set #1
bqmodel:isDerivedFrom BioModels Database Kholodenko1999 - EGFR signaling
BioModels Database Schoeberl2002_EGF_MAPK
BioModels Database Kholodenko2000 - Ultrasensitivity and negative feedback bring oscillations in MAPK cascade
PubMed 11772030
set #2
bqbiol:hasProperty Mathematical Modelling Ontology MAMO_0000046
set #3
bqbiol:isVersionOf Gene Ontology ERBB signaling pathway
set #4
bqbiol:hasPart Gene Ontology regulation of protein kinase B signaling
Gene Ontology regulation of MAP kinase activity
bqbiol:hasTaxon Taxonomy Cricetinae
Notes

Figure4 and Figure5 can be simulated by Copasi. Figure4 can be simulated in MathSBML as well. There are some typos in the paper:K29=234, is it should k_29; Table2, reaction17, is there are "slash" missing in between the rate equation; reaction 33,"Akt-PI-PP" in the last term of denominator instead of "AktPI-P" . For plotting figure4, we create another extra parameter *_percent, and use assignment rule calculate percentage of each species.


To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.


To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 12691603 Submission Date: 06 Sep 2007 08:06:00 UTC Last Modification Date: 26 May 2014 23:17:39 UTC Creation Date: 16 Jul 2008 13:00:01 UTC
Mathematical expressions
Reactions
reaction_0000001 reaction_0000002 reaction_0000003 reaction_0000004
reaction_0000005 reaction_0000006 reaction_0000007 reaction_0000008
reaction_0000009 reaction_0000010 reaction_0000011 reaction_0000012
reaction_0000013 reaction_0000014 reaction_0000015 reaction_0000016
reaction_0000017 reaction_0000018 reaction_0000019 reaction_0000020
reaction_0000021 reaction_0000022 reaction_0000023 reaction_0000024
reaction_0000025 reaction_0000026 reaction_0000029 reaction_0000028
reaction_0000027 reaction_0000030 reaction_0000031 reaction_0000032
reaction_0000033 reaction_0000034    
Rules
Assignment Rule (variable: RP_percent) Assignment Rule (variable: ERKPP_percent) Assignment Rule (variable: AktPP_percent) Assignment Rule (variable: MEKPP_percent)
Assignment Rule (variable: ShP_percent) Assignment Rule (variable: PI3Kstar_percent) Assignment Rule (variable: Rafstar_percent)  
Physical entities
Compartments Species
cell Akt AktPIP3 AktPIP
AktPIPP ERK ERKP
ERKPP GS HRG
MEK MEKP MEKPP
PI3K PI3Kstar PIP3
R RP RHRG
RHRG2 RPI3K RPI3Kstar
RShGS RShP RShc
Raf Rafstar RasGDP
RasGTP ShGS ShP
Shc P_I internalization
E MKP3 PP2A
Global parameters
k1 k2 k3 k5
k6 k7 k8 k9
V10 k11 V12 k13
k14 k15 k16 k17
k20 k18 k19 k21
k22 k23 k24 k25
k27 V26 V28 k29
V30 k31 V32 k33
k34 k_1 k_2 k_3
K4 k_5 k_6 k_7
k_8 k_9 K10 K11
K12 K13 K14 K15
K18 K19 K20 K21
K22 k_23 k_24 k_25
K26 K27 K28 K30
K31 K32 K33 k_34
V4 K17 K16 k_29
RP_percent AktPP_percent MEKPP_percent ERKPP_percent
Rafstar_percent ShP_percent PI3Kstar_percent  
Reactions (34)
 
 reaction_0000001 [R] + [HRG] ↔ [RHRG];  
 
 reaction_0000002 2.0 × [RHRG] ↔ [RHRG2];  
 
 reaction_0000003 [RHRG2] ↔ [RP];  
 
 reaction_0000004 [RP] → [RHRG2];  
 
 reaction_0000005 [RP] + [Shc] ↔ [RShc];  
 
 reaction_0000006 [RShc] ↔ [RShP];  
 
 reaction_0000007 [RShP] + [GS] ↔ [RShGS];  
 
 reaction_0000008 [RShGS] ↔ [ShGS] + [RP];  
 
 reaction_0000009 [ShGS] ↔ [GS] + [ShP];  
 
 reaction_0000010 [ShP] → [Shc];  
 
 reaction_0000011 [RasGDP] → [RasGTP];   {ShGS}
 
 reaction_0000012 [RasGTP] → [RasGDP];  
 
 reaction_0000013 [Raf] → [Rafstar];   {RasGTP}
 
 reaction_0000014 [Rafstar] → [Raf];   {AktPIPP} , {E}
 
 reaction_0000015 [MEK] → [MEKP];   {Rafstar}
 
 reaction_0000016 [MEKP] → [MEK];   {MEKPP} , {AktPIP} , {AktPIPP} , {PP2A}
 
 reaction_0000017 [MEKP] → [MEKPP];   {MEK} , {Rafstar}
 
 reaction_0000018 [MEKPP] → [MEKP];   {AktPIP} , {AktPIPP} , {PP2A}
 
 reaction_0000019 [ERK] → [ERKP];   {MEKPP}
 
 reaction_0000020 [ERKP] → [ERK];   {ERKPP} , {MKP3}
 
 reaction_0000021 [ERKP] → [ERKPP];   {MEKPP} , {ERK}
 
 reaction_0000022 [ERKPP] → [ERKP];   {MKP3}
 
 reaction_0000023 [RP] + [PI3K] ↔ [RPI3K];  
 
 reaction_0000024 [RPI3K] ↔ [RPI3Kstar];  
 
 reaction_0000025 [RPI3Kstar] ↔ [RP] + [PI3Kstar];  
 
 reaction_0000026 [PI3Kstar] → [PI3K];  
 
 reaction_0000029 [PIP3] + [Akt] ↔ [AktPIP3];  
 
 reaction_0000028 [PIP3] → [P_I];  
 
 reaction_0000027 [P_I] → [PIP3];   {PI3Kstar}
 
 reaction_0000030 [AktPIP3] → [AktPIP];  
 
 reaction_0000031 [AktPIP] → [AktPIP3];   {MEKP} , {MEKPP} , {AktPIPP} , {PP2A}
 
 reaction_0000032 [AktPIP] → [AktPIPP];   {AktPIP3}
 
 reaction_0000033 [AktPIPP] → [AktPIP];   {MEKP} , {MEKPP} , {PP2A}
 
 reaction_0000034 [RP] ↔ [internalization];  
 
Rules (7)
 
 Assignment Rule (name: RP_percent) RP_percent = (RP+RPI3K+RPI3Kstar+RShGS+RShP+RShc)*200/80
 
 Assignment Rule (name: ERKPP_percent) ERKPP_percent = ERKPP*100/1000
 
 Assignment Rule (name: AktPP_percent) AktPP_percent = AktPIPP*100/10
 
 Assignment Rule (name: MEKPP_percent) MEKPP_percent = MEKPP*100/120
 
 Assignment Rule (name: ShP_percent) ShP_percent = ShP*100/1000
 
 Assignment Rule (name: PI3Kstar_percent) PI3Kstar_percent = PI3Kstar*100/10
 
 Assignment Rule (name: Rafstar_percent) Rafstar_percent = Rafstar*100/100
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 Akt
Compartment: cell
Initial concentration: 10.0
 
 AktPIP3
Compartment: cell
Initial concentration: 0.0
 
 AktPIP
Compartment: cell
Initial concentration: 0.0
 
 AktPIPP
Compartment: cell
Initial concentration: 0.0
 
 ERK
Compartment: cell
Initial concentration: 1000.0
 
 ERKP
Compartment: cell
Initial concentration: 0.0
 
 ERKPP
Compartment: cell
Initial concentration: 0.0
 
   GS
Compartment: cell
Initial concentration: 10.0
 
 HRG
Compartment: cell
Initial concentration: 330.0
 
 MEK
Compartment: cell
Initial concentration: 120.0
 
 MEKP
Compartment: cell
Initial concentration: 0.0
 
 MEKPP
Compartment: cell
Initial concentration: 0.0
 
 PI3K
Compartment: cell
Initial concentration: 10.0
 
 PI3Kstar
Compartment: cell
Initial concentration: 0.0
 
 PIP3
Compartment: cell
Initial concentration: 0.0
 
 R
Compartment: cell
Initial concentration: 80.0
 
 RP
Compartment: cell
Initial concentration: 0.0
 
 RHRG
Compartment: cell
Initial concentration: 0.0
 
 RHRG2
Compartment: cell
Initial concentration: 0.0
 
 RPI3K
Compartment: cell
Initial concentration: 0.0
 
 RPI3Kstar
Compartment: cell
Initial concentration: 0.0
 
   RShGS
Compartment: cell
Initial concentration: 0.0
 
   RShP
Compartment: cell
Initial concentration: 0.0
 
   RShc
Compartment: cell
Initial concentration: 0.0
 
 Raf
Compartment: cell
Initial concentration: 100.0
 
 Rafstar
Compartment: cell
Initial concentration: 0.0
 
 RasGDP
Compartment: cell
Initial concentration: 120.0
 
 RasGTP
Compartment: cell
Initial concentration: 0.0
 
   ShGS
Compartment: cell
Initial concentration: 0.0
 
   ShP
Compartment: cell
Initial concentration: 0.0
 
 Shc
Compartment: cell
Initial concentration: 1000.0
 
 P_I
Compartment: cell
Initial concentration: 800.0
 
   internalization
Compartment: cell
Initial concentration: 0.0
 
   E
Compartment: cell
Initial concentration: 7.0
Constant
 
 MKP3
Compartment: cell
Initial concentration: 2.4
Constant
 
 PP2A
Compartment: cell
Initial concentration: 11.4
Constant
 
Global Parameters (75)
 
   k1
Value: 0.0012
Constant
 
   k2
Value: 0.01
Constant
 
   k3
Value: 1.0
Constant
 
   k5
Value: 0.1
Constant
 
   k6
Value: 20.0
Constant
 
   k7
Value: 60.0
Constant
 
   k8
Value: 2040.0
Constant
 
   k9
Value: 40.8
Constant
 
   V10
Value: 0.0154
Constant
 
   k11
Value: 0.222
Constant
 
   V12
Value: 0.289
Constant
 
   k13
Value: 1.53
Constant
 
   k14
Value: 0.00673
Constant
 
   k15
Value: 3.5
Constant
 
   k16
Value: 0.058
Constant
 
   k17
Value: 2.9
Constant
 
   k20
Value: 0.3
Constant
 
   k18
Value: 0.058
Constant
 
   k19
Value: 9.5
Constant
 
   k21
Value: 16.0
Constant
 
   k22
Value: 0.27
Constant
 
   k23
Value: 0.1
Constant
 
   k24
Value: 9.85
Constant
 
   k25
Value: 45.8
Constant
 
   k27
Value: 16.9
Constant
 
   V26
Value: 2620.0
Constant
 
   V28
Value: 17000.0
Constant
 
   k29
Value: 507.0
Constant
 
   V30
Value: 20000.0
Constant
 
   k31
Value: 0.107
Constant
 
   V32
Value: 20000.0
Constant
 
   k33
Value: 0.211
Constant
 
   k34
Value: 0.0010
Constant
 
   k_1
Value: 7.6E-4
Constant
 
   k_2
Value: 0.1
Constant
 
   k_3
Value: 0.01
Constant
 
   K4
Value: 50.0
Constant
 
   k_5
Value: 1.0
Constant
 
   k_6
Value: 5.0
Constant
 
   k_7
Value: 546.0
Constant
 
   k_8
Value: 15700.0
Constant
 
   k_9
Constant
 
   K10
Value: 340.0
Constant
 
   K11
Value: 0.181
Constant
 
   K12
Value: 0.0571
Constant
 
   K13
Value: 11.7
Constant
 
   K14
Value: 8.07
Constant
 
   K15
Value: 317.0
Constant
 
   K18
Value: 60.0
Constant
 
   K19
Value: 146000.0
Constant
 
   K20
Value: 160.0
Constant
 
   K21
Value: 146000.0
Constant
 
   K22
Value: 60.0
Constant
 
   k_23
Value: 2.0
Constant
 
   k_24
Value: 0.0985
Constant
 
   k_25
Value: 0.047
Constant
 
   K26
Value: 3680.0
Constant
 
   K27
Value: 39.1
Constant
 
   K28
Value: 9.02
Constant
 
   K30
Value: 80000.0
Constant
 
   K31
Value: 4.35
Constant
 
   K32
Value: 80000.0
Constant
 
   K33
Value: 12.0
Constant
 
   k_34
Constant
 
   V4
Value: 62.5
Constant
 
   K17
Value: 317.0
Constant
 
   K16
Value: 2200.0
Constant
 
   k_29
Value: 234.0
Constant
 
   RP_percent
Value: NaN
 
   AktPP_percent
Value: NaN
 
   MEKPP_percent
Value: NaN
 
   ERKPP_percent
Value: NaN
 
   Rafstar_percent
Value: NaN
 
   ShP_percent
Value: NaN
 
   PI3Kstar_percent
Value: NaN
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000146

Curator's comment: (updated: 28 Aug 2007 00:16:43 BST)

Figure4 has been reproduced by MathSBML.

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