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name: 10
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product: 160045
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160110
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COPASI20
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159059
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W3 CDTF: Wed May 22 14:49:01 BST 2013

159336
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COPASI18
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159023
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COPASI6
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COPASI19
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COPASI9
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COPASI8
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COPASI24
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160852
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COPASI23
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COPASI14
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159928
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160370
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COPASI5
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COPASI22
reversible: false
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is version of: GO:0002181
fast: false
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160253
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159480
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COPASI15
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name: 6
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160201
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BIOMD0000000443
reaction: COPASI25
reaction: COPASI28
species: 159156
name: function_4_5_1
species: 159097
notes: Sarma2012 - Oscillations in MAPK cascade (S1n) Two plausible designs (S1 and S2) of coupled positive and negative feedback loops of MAPK cascade has been described in this paper. Further these models were extended to S1n and S2n, to incorporate the nuclear-cytoplasmic translocation of the MK layer components of the cascade. This model corresponds to model S1n that comprises negative feedback from MK-PP to MKKK-P layer coupled to positive feedback from MK-PP to MKK-PP layer, with the inclusion of nuclear-cytoplasmic translocation. This model is described in the article: Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops. Sarma U, Ghosh I. BMC Res Notes. 2012 Jun 13;5:287. Abstract: BACKGROUND: Feedback loops, both positive and negative are embedded in the Mitogen Activated Protein Kinase (MAPK) cascade. In the three layer MAPK cascade, both feedback loops originate from the terminal layer and their sites of action are either of the two upstream layers. Recent studies have shown that the cascade uses coupled positive and negative feedback loops in generating oscillations. Two plausible designs of coupled positive and negative feedback loops can be elucidated from the literature; in one design the positive feedback precedes the negative feedback in the direction of signal flow and vice-versa in another. But it remains unexplored how the two designs contribute towards triggering oscillations in MAPK cascade. Thus it is also not known how amplitude, frequency, robustness or nature (analogous/digital) of the oscillations would be shaped by these two designs. RESULTS: We built two models of MAPK cascade that exhibited oscillations as function of two underlying designs of coupled positive and negative feedback loops. Frequency, amplitude and nature (digital/analogous) of oscillations were found to be differentially determined by each design. It was observed that the positive feedback emerging from an oscillating MA…
name: function_4_10_1
reaction: COPASI14
species: COPASI5
name: function_4_3_1
species: COPASI4
is: MODEL1112190006
function def: 158939
units def: 158975
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units def: 158999
name: function_4_2_1
reaction: COPASI17
name: function_4_4_1
name: 12
species: 159047
function def: COPASI37
function def: 158951
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type: SBMLModel
reaction: COPASI26
name: 15
function def: COPASI34
compartment: 159023
substance units: 158999
reaction: COPASI10
function def: COPASI30
species: COPASI8
is described by: http://identifiers.org/pubmed/22694947
name: Sarma2012 - Oscillations in MAPK cascade (S1n)
reaction: COPASI29
species: COPASI3
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name: 22
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species: 159059
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species: 159120
reaction: COPASI18
function def: 158891
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curated: true
species: COPASI7
reaction: 159384
reaction: COPASI9
function def: COPASI35
species: COPASI6
reaction: COPASI23
reaction: COPASI27
function def: COPASI31
area units: area
function def: COPASI36
name: 21
species: 159108
function def: 158963
function def: COPASI32
name: function_4_8_1
reaction: COPASI11
species: 159083
species: 159144
is: GO:0000165
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name: function_4_1_1
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function def: 158915
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reaction: COPASI12
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reaction: COPASI13
is: http://identifiers.org/taxonomy/131567
reaction: COPASI16

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COPASI21
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COPASI4
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159011
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COPASI28
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160876
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160292
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159672
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COPASI10
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COPASI26
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COPASI11
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COPASI25
is version of: GO:0051169
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given: Nick
family: Juty

orgname: EMBL-EBI

W3 CDTF: Mon Mar 18 14:07:04 GMT 2013

orgname: National Centre for Cell Science

given: Uddipan
family: Sarma

orgname: EMBL-EBI

n:
  given: Vijayalakshmi
  family: Chelliah