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BIOMD0000000116 - McClean2007_CrossTalk

 

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Reference Publication
Publication ID: 17259986
McClean MN, Mody A, Broach JR, Ramanathan S.
Cross-talk and decision making in MAP kinase pathways.
Nat. Genet. 2007 Mar; 39(3): 409-414
FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.  [more]
Model
Original Model: BIOMD0000000116.xml.origin
Submitter: Christian Waltermann
Submission ID: MODEL7321452458
Submission Date: 05 Jun 2007 21:06:06 UTC
Last Modification Date: 05 Jul 2012 16:32:26 UTC
Creation Date: 08 May 2007 09:29:14 UTC
Encoders:  Enuo He
   Christian Waltermann
set #1
bqbiol:isVersionOf Gene Ontology response to pheromone
Gene Ontology MAPK cascade involved in osmosensory signaling pathway
bqbiol:occursIn Taxonomy Saccharomyces cerevisiae
Notes

This model encoded according to the paper Cross-talk and decision making in MAP kinase pathways. Supplementary Figure 2 has been reproduced by COPASI4.0.20 (development) using parameter scan method. You probably need to uncheck "always use initial conditions" in copasi when you simulate for the second run in order to get the figure. S1 scale from 0 to 12. Keep in mind that the y axis is the fractions of excited X3 and Y3, meaning that X3P and Y3P are normalized by total concentration X3T and Y3T.

The results from modeling the pathway in Supplementary Figure1a, including both activation and inhibition. According to the paper, the value of ka and kd should in the orange region (ka belongs [0,1], kd belongs [1,10]) so assigned ka=0, kd=1.

The author made the simplifying assumption that the interactions between the pathways are symmetric. Thus the k12xy=k12yx=ka, k33xy=k33yx=kd.


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: 17259986 Submission Date: 05 Jun 2007 21:06:06 UTC Last Modification Date: 05 Jul 2012 16:32:26 UTC Creation Date: 08 May 2007 09:29:14 UTC
Mathematical expressions
Reactions
X1 activats X2 S1 activates X1 X2 activates X3 S2 activates Y1
Y1p activates Y2p Y2p activates Y3p X1p activates Y2p Y1p activates X2p
X3p inhibited by Y3p Y3p inhibited by X3p    
Physical entities
Compartments Species
cell X1p X2p X3p
Y1p Y2p Y3p
Global parameters
X1T X2T X3T Y1T
Y2T Y3T kx S1
Kmx k12x k23x kd
ka Kmyx S2 ky
Kmy k12y k23y Kmxy
Reactions (10)
 
 X1 activats X2 [X1p] → [X2p];  
 
 S1 activates X1  → [X1p];  
 
 X2 activates X3 [X2p] → [X3p];  
 
 S2 activates Y1  → [Y1p];  
 
 Y1p activates Y2p [Y1p] → [Y2p];  
 
 Y2p activates Y3p [Y2p] → [Y3p];  
 
 X1p activates Y2p [X1p] → [Y2p];  
 
 Y1p activates X2p [Y1p] → [X2p];  
 
 X3p inhibited by Y3p [X3p] → ;   {Y3p}
 
 Y3p inhibited by X3p [Y3p] → ;   {X3p}
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 X1p
Compartment: cell
Initial concentration: 1.023667
 
 X2p
Compartment: cell
Initial concentration: 2.154231
 
 X3p
Compartment: cell
Initial concentration: 6.271793
 
 Y1p
Compartment: cell
Initial concentration: 3.203692
 
 Y2p
Compartment: cell
Initial concentration: 8.232192
 
 Y3p
Compartment: cell
Initial concentration: 9.312021
 
Global Parameters (20)
 
   X1T
Value: 10.0
Constant
 
   X2T
Value: 10.0
Constant
 
   X3T
Value: 10.0
Constant
 
   Y1T
Value: 10.0
Constant
 
   Y2T
Value: 10.0
Constant
 
   Y3T
Value: 10.0
Constant
 
   kx
Value: 1.0
Constant
 
 S1
Value: 8.5
Constant
 
   Kmx
Value: 1.0
Constant
 
   k12x
Value: 1.0
Constant
 
   k23x
Value: 1.0
Constant
 
   kd
Value: 1.0
Constant
 
   ka
Constant
 
   Kmyx
Value: 1.0
Constant
 
   S2
Value: 5.0
Constant
 
   ky
Value: 1.0
Constant
 
   Kmy
Value: 1.0
Constant
 
   k12y
Value: 1.0
Constant
 
   k23y
Value: 1.0
Constant
 
   Kmxy
Value: 1.0
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000116

Curator's comment: (updated: 30 May 2007 19:26:06 BST)

Supplementary Figure 2 has been reproduced by COPASI4.0.20 (development) using parameter scan method. You probably need to uncheck "always use initial conditions" in copasi when you simulate for the second run in order to get the figure. S1 scale from 0 to 12.

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