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BIOMD0000000477 - Mol2013 - Immune Signal Transduction in Leishmaniasis

 

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Reference Publication
Publication ID: 23994140
Mol M, Patole MS, Singh S.
Immune signal transduction in leishmaniasis from natural to artificial systems: role of feedback loop insertion.
Biochim. Biophys. Acta 2014 Jan; 1840(1): 71-79
National Centre for Cell Science, NCCS Complex, Ganeshkhind, Pune University Campus, Pune 411007, India.  [more]
Model
Original Model: BIOMD0000000477.origin
Submitter: Shailza Singh
Submission ID: MODEL1308080000
Submission Date: 08 Aug 2013 11:13:47 UTC
Last Modification Date: 10 Oct 2014 11:11:26 UTC
Creation Date: 10 Sep 2013 14:43:01 UTC
Encoders:  Nick Juty
   Vijayalakshmi Chelliah
   Milsee Mol
set #1
bqbiol:hasProperty Human Disease Ontology leishmaniasis
set #2
bqbiol:hasPart Reactome REACT_9417.7
set #3
bqbiol:isVersionOf Gene Ontology immune response-regulating signaling pathway
set #4
bqbiol:hasTaxon Taxonomy Homo sapiens
Notes

Created by The MathWorks, Inc. SimBiology tool, Version 3.3

Model
Publication ID: 23994140 Submission Date: 08 Aug 2013 11:13:47 UTC Last Modification Date: 10 Oct 2014 11:11:26 UTC Creation Date: 10 Sep 2013 14:43:01 UTC
Mathematical expressions
Reactions
1 2 3 4
5 6 7 8
9 10 11 12
13 14 15 16
17 18 19 20
21 22 23 24
25 26 27 28
29 30 31 32
33 34 35 36
37 38 39 40
41 42 43 44
45 46 47 48
49      
Physical entities
Compartments Species
cytoplasm TNF TNFR1 TRADD_TRAF2_RIP
IkB NIK IkK_NFkB
NFkB MEKK1 MKK4/7
JNK ASK p38
LPG CD14-TLR MyD88
IRAK1/4 TRAF6 TAB2_TAK1_TAB1
MKK1/2 ERK1/2 MKK3/6
EGF EGFR PLC gamma
PIP2 DAG PKC
PI3K Akt Shc/Grb2/Sos1
Ras Raf JAK
STAT1/3    
nucleus NFkB JNK cjun
p38 cfos ERK1/2
Akt STAT1/3 TNF
Reactions (49)
 
 1 [TNF] → [TNFR1];   {TNF}
 
 2 [TNFR1] → [TRADD_TRAF2_RIP];   {TNFR1}
 
 3 [TRADD_TRAF2_RIP] → [NIK];   {TRADD_TRAF2_RIP}
 
 4 [TRADD_TRAF2_RIP] → [MEKK1];   {TRADD_TRAF2_RIP}
 
 5 [NIK] → [IkB];   {NIK}
 
 6 [IkK_NFkB] → [NFkB];   {IkK_NFkB}
 
 7 [NFkB] → [NFkB];   {NFkB}
 
 8 [IkB] → [IkK_NFkB];   {IkB}
 
 9 [MEKK1] → [MKK4/7];   {MEKK1}
 
 10 [MKK4/7] → [JNK];   {MKK4/7}
 
 11 [JNK] → [JNK];   {JNK}
 
 12 [JNK] → [cjun];   {JNK}
 
 13 [TRADD_TRAF2_RIP] → [ASK];   {TRADD_TRAF2_RIP}
 
 14 [ASK] → [MKK3/6];   {ASK}
 
 15 [p38] → [p38];   {p38}
 
 16 [p38] → [cfos];   {p38}
 
 17 [LPG] → [CD14-TLR];   {LPG}
 
 18 [CD14-TLR] → [MyD88];   {CD14-TLR}
 
 19 [MyD88] → [IRAK1/4];   {MyD88}
 
 20 [IRAK1/4] → [TRAF6];   {IRAK1/4}
 
 21 [TRAF6] → [TAB2_TAK1_TAB1];   {TRAF6}
 
 22 [TAB2_TAK1_TAB1] → [NIK];   {TAB2_TAK1_TAB1}
 
 23 [TAB2_TAK1_TAB1] → [MKK1/2];   {TAB2_TAK1_TAB1}
 
 24 [MKK1/2] → [ERK1/2];   {MKK1/2}
 
 25 [ERK1/2] → [ERK1/2];   {ERK1/2}
 
 26 [TAB2_TAK1_TAB1] → [MKK4/7];   {TAB2_TAK1_TAB1}
 
 27 [TAB2_TAK1_TAB1] → [MKK3/6];   {TAB2_TAK1_TAB1}
 
 28 [MKK3/6] → [p38];   {MKK3/6}
 
 29 [EGF] → [EGFR];   {EGF}
 
 30 [EGFR] → [PLC gamma];   {EGFR}
 
 31 [PLC gamma] → [PIP2];   {PLC gamma}
 
 32 [PIP2] → [DAG];   {PIP2}
 
 33 [DAG] → [PKC];   {DAG}
 
 34 [PKC] → [IkK_NFkB];   {PKC}
 
 35 [EGFR] → [PI3K];   {EGFR}
 
 36 [PI3K] → [Akt];   {PI3K}
 
 37 [Akt] → [Akt];   {Akt}
 
 38 [EGFR] → [Shc/Grb2/Sos1];   {EGFR}
 
 39 [Shc/Grb2/Sos1] → [Ras];   {Shc/Grb2/Sos1}
 
 40 [Ras] → [Raf];   {Ras}
 
 41 [Raf] → [MKK1/2];   {Raf}
 
 42 [Ras] → [MKK4/7];   {Ras}
 
 43 [EGFR] → [JAK];   {EGFR}
 
 44 [JAK] → [STAT1/3];   {JAK}
 
 45 [STAT1/3] → [STAT1/3];   {STAT1/3}
 
 46 [NFkB] → [TNF];   {NFkB}
 
 47 [TNF] → [TNF];   {TNF}
 
 48 [PKC] → [Ras];   {PKC}
 
 49 [PKC] → [Raf];   {PKC}
 
   cytoplasm Spatial dimensions: 3.0  Compartment size: 1.0
 
 TNF
Compartment: cytoplasm
Initial amount: 1.5  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 TNFR1
Compartment: cytoplasm
Initial amount: 1.3  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 TRADD_TRAF2_RIP
Compartment: cytoplasm
Initial amount: 1.3  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 IkB
Compartment: cytoplasm
Initial amount: 0.8  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 NIK
Compartment: cytoplasm
Initial amount: 1.5  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 IkK_NFkB
Compartment: cytoplasm
Initial amount: 1.4  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 NFkB
Compartment: cytoplasm
Initial amount: 1.2  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 MEKK1
Compartment: cytoplasm
Initial amount: 1.4  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 MKK4/7
Compartment: cytoplasm
Initial amount: 1.2  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 JNK
Compartment: cytoplasm
Initial amount: 1.2  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 ASK
Compartment: cytoplasm
Initial amount: 1.5  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 p38
Compartment: cytoplasm
Initial amount: 0.9  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 LPG
Compartment: cytoplasm
Initial amount: 1.5  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 CD14-TLR
Compartment: cytoplasm
Initial amount: 1.5  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 MyD88
Compartment: cytoplasm
Initial amount: 0.85  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 IRAK1/4
Compartment: cytoplasm
Initial amount: 1.0  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 TRAF6
Compartment: cytoplasm
Initial amount: 1.1  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 TAB2_TAK1_TAB1
Compartment: cytoplasm
Initial amount: 1.3  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 MKK1/2
Compartment: cytoplasm
Initial amount: 1.1  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 ERK1/2
Compartment: cytoplasm
Initial amount: 0.8  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 MKK3/6
Compartment: cytoplasm
Initial amount: 1.5  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 EGF
Compartment: cytoplasm
Initial amount: 1.6  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 EGFR
Compartment: cytoplasm
Initial amount: 1.3  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 PLC gamma
Compartment: cytoplasm
Initial amount: 1.6  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 PIP2
Compartment: cytoplasm
Initial amount: 1.45  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 DAG
Compartment: cytoplasm
Initial amount: 0.9  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 PKC
Compartment: cytoplasm
Initial amount: 1.5  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 PI3K
Compartment: cytoplasm
Initial amount: 1.6  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 Akt
Compartment: cytoplasm
Initial amount: 1.2  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 Shc/Grb2/Sos1
Compartment: cytoplasm
Initial amount: 0.3  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 Ras
Compartment: cytoplasm
Initial amount: 1.2  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 Raf
Compartment: cytoplasm
Initial amount: 1.2  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 JAK
Compartment: cytoplasm
Initial amount: 1.6  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 STAT1/3
Compartment: cytoplasm
Initial amount: 1.1  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
   nucleus Spatial dimensions: 3.0  Compartment size: 1.0
 
 NFkB
Compartment: nucleus
Initial amount: 0.2  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 JNK
Compartment: nucleus
Initial amount: 0.6  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 cjun
Compartment: nucleus
Initial amount: 0.91  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 p38
Compartment: nucleus
Initial amount: 0.8  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 cfos
Compartment: nucleus
Initial amount: 0.5  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 ERK1/2
Compartment: nucleus
Initial amount: 0.0  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 Akt
Compartment: nucleus
Initial amount: 0.0  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 STAT1/3
Compartment: nucleus
Initial amount: 0.0  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
 TNF
Compartment: nucleus
Initial amount: 0.0  (Units: MWBUILTINPREFIX_nano_MWBUILTINUNIT_mole)
 
1 (1)
 
   k1
Value: 1.2   (Units: 1/second)
Constant
 
2 (1)
 
   k2
Value: 1.18   (Units: 1/second)
Constant
 
3 (2)
 
   k3
Value: 0.6   (Units: nanomole)
Constant
 
   v3
Value: 0.6   (Units: nanomole/second)
Constant
 
4 (2)
 
   v4
Value: 0.28   (Units: nanomole/second)
Constant
 
   k4
Value: 1.5   (Units: nanomole)
Constant
 
5 (2)
 
   k5
Value: 0.15   (Units: nanomole)
Constant
 
   v5
Value: 1.3   (Units: nanomole/second)
Constant
 
6 (2)
 
   k6
Value: 0.1   (Units: nanomole)
Constant
 
   v6
Value: 2.2   (Units: nanomole/second)
Constant
 
7 (1)
 
   k7
Value: 1.4   (Units: 1/second)
Constant
 
8 (2)
 
   k8
Value: 0.56   (Units: nanomole)
Constant
 
   v8
Value: 1.3   (Units: nanomole/second)
Constant
 
9 (2)
 
   v9
Value: 0.6   (Units: nanomole/second)
Constant
 
   k9
Value: 0.2   (Units: nanomole)
Constant
 
10 (2)
 
   v10
Value: 0.98   (Units: nanomole/second)
Constant
 
   k10
Value: 0.15   (Units: nanomole)
Constant
 
11 (1)
 
   k11
Value: 0.61   (Units: 1/second)
Constant
 
12 (2)
 
   v12
Value: 1.14   (Units: nanomole/second)
Constant
 
   k12
Value: 0.62   (Units: nanomole)
Constant
 
13 (2)
 
   k13
Value: 0.08   (Units: nanomole)
Constant
 
   v13
Value: 0.99   (Units: nanomole/second)
Constant
 
14 (2)
 
   v14
Value: 1.2   (Units: nanomole/second)
Constant
 
   k14
Value: 0.02   (Units: nanomole)
Constant
 
15 (1)
 
   k15
Value: 1.0   (Units: 1/second)
Constant
 
16 (2)
 
   v16
Value: 1.5   (Units: nanomole/second)
Constant
 
   k16
Value: 0.2   (Units: nanomole)
Constant
 
17 (1)
 
   k17
Value: 0.6   (Units: 1/second)
Constant
 
18 (1)
 
   k18
Value: 2.0   (Units: 1/second)
Constant
 
19 (1)
 
   k19
Value: 0.72   (Units: 1/second)
Constant
 
20 (1)
 
   k20
Value: 0.55   (Units: 1/second)
Constant
 
21 (1)
 
   k21
Value: 0.48   (Units: 1/second)
Constant
 
22 (2)
 
   v22
Value: 0.5   (Units: nanomole/second)
Constant
 
   k22
Value: 0.2   (Units: nanomole)
Constant
 
23 (2)
 
   v23
Value: 0.2   (Units: nanomole/second)
Constant
 
   k23
Value: 0.01   (Units: nanomole)
Constant
 
24 (2)
 
   v24
Value: 0.9   (Units: nanomole/second)
Constant
 
   k24
Value: 0.2   (Units: nanomole)
Constant
 
25 (1)
 
   k25
Value: 0.42   (Units: 1/second)
Constant
 
26 (2)
 
   v26
Value: 0.3   (Units: nanomole/second)
Constant
 
   k26
Value: 0.01   (Units: nanomole)
Constant
 
27 (2)
 
   v27
Value: 0.1   (Units: nanomole/second)
Constant
 
   k27
Value: 0.01   (Units: nanomole)
Constant
 
28 (2)
 
   v28
Value: 1.5   (Units: nanomole/second)
Constant
 
   k28
Value: 0.03   (Units: nanomole)
Constant
 
29 (1)
 
   k29
Value: 0.6   (Units: 1/second)
Constant
 
30 (2)
 
   v30
Value: 2.0E-4   (Units: nanomole/second)
Constant
 
   k30
Value: 0.5   (Units: nanomole)
Constant
 
31 (2)
 
   v31
Value: 0.6   (Units: nanomole/second)
Constant
 
   k31
Value: 1.0   (Units: nanomole)
Constant
 
32 (2)
 
   v32
Value: 0.9   (Units: nanomole/second)
Constant
 
   k32
Value: 0.3   (Units: nanomole)
Constant
 
33 (1)
 
   k33
Value: 0.35   (Units: 1/second)
Constant
 
34 (2)
 
   v34
Value: 1.2   (Units: nanomole/second)
Constant
 
   k34
Value: 0.2   (Units: nanomole)
Constant
 
35 (2)
 
   v35
Value: 0.2   (Units: nanomole/second)
Constant
 
   k35
Value: 0.8   (Units: nanomole)
Constant
 
36 (2)
 
   v36
Value: 0.8   (Units: nanomole/second)
Constant
 
   k36
Value: 1.5   (Units: nanomole)
Constant
 
37 (1)
 
   k37
Value: 0.2   (Units: 1/second)
Constant
 
38 (1)
 
   k38
Value: 0.299   (Units: 1/second)
Constant
 
39 (2)
 
   v39
Value: 0.24   (Units: nanomole/second)
Constant
 
   k39
Value: 1.2   (Units: nanomole)
Constant
 
40 (2)
 
   v40
Value: 0.2   (Units: nanomole/second)
Constant
 
   k40
Value: 1.5   (Units: nanomole)
Constant
 
41 (2)
 
   v41
Value: 0.7   (Units: nanomole/second)
Constant
 
   k41
Value: 1.5   (Units: nanomole)
Constant
 
42 (2)
 
   v42
Value: 0.4   (Units: nanomole/second)
Constant
 
   k42
Value: 1.5   (Units: nanomole)
Constant
 
43 (2)
 
   v43
Value: 0.01   (Units: nanomole/second)
Constant
 
   k43
Value: 1.8   (Units: nanomole)
Constant
 
44 (2)
 
   v44
Value: 1.0   (Units: nanomole/second)
Constant
 
   k44
Value: 1.5   (Units: nanomole)
Constant
 
45 (1)
 
   k45
Value: 0.19   (Units: 1/second)
Constant
 
46 (3)
 
   v46
Value: 2.35   (Units: nanomole/second)
Constant
 
   n46
Value: 1.0
Constant
 
   kp47
Value: 0.43   (Units: nanomole)
Constant
 
47 (1)
 
   k47
Value: 1.1   (Units: 1/second)
Constant
 
48 (2)
 
   v48
Value: 1.0   (Units: nanomole/second)
Constant
 
   k48
Value: 1.0   (Units: nanomole)
Constant
 
49 (2)
 
   v49
Value: 1.0   (Units: nanomole/second)
Constant
 
   k49
Value: 1.0   (Units: nanomole)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000477

Curator's comment: (updated: 10 Sep 2013 15:50:35 BST)

The paper has a Flux V/s Sensitivity bar chart (figure 5) of the signalling components that are at the crosstalk points and those that show high PCA (Principal component analysis) score. Here, time-course of the fluxes of the corresponding components (components at the crosstalk points and the components that show high PCA score) of figure 5 of the papers is produced. Simulation was done using Copasi v4.10 (Build 55). The plots were generated using Gnuplot.

Additional file(s)
  • Reaction Fluxes:
    Reaction fluxes of signalling components that are at the crosstalk point and that show high PCA score.
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