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type: Parameter

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metaid_0000060
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metaid_0000018
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361912
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361984
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metaid_0000024
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metaid_0000047
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has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000035
type: Species

metaid_0000004
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metaid_0000057
kinetic law: 362165
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is version of: GO:0030163
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361671
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metaid_0000019
constant: true
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type: Parameter

metaid_0000037
encodes: Q8N7R0
is version of: ENSG00000176654
constant: false
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has only substance units: false
initial concentration: NaN
initial amount: 0.0
in compartment: metaid_0000035
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metaid_0000013
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362092
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metaid_0000023
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361767
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metaid_0000054
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is version of: GO:0010467
reversible: false

metaid_0000003
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is version of: GO:0010467
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metaid_0000034
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metaid_0000012
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metaid_0000022
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type: Parameter

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metaid_0000032
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metaid_0000008
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362056
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metaid_0000015
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metaid_0000021
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type: Parameter

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metaid_0000028
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is version of: GO:0030163
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metaid_0000044
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362140
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metaid_0000058
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361948
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metaid_0000038
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metaid_0000050
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metaid_0000031
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362153
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metaid_0000007
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metaid_0000026
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361683
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metaid_0000059
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metaid_0000045
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BIOMD0000000203
compartment: metaid_0000035
reaction: metaid_0000051
reaction: metaid_0000048
parameter: metaid_0000032
parameter: metaid_0000017
reaction: metaid_0000052
reaction: metaid_0000055
reaction: metaid_0000049
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volume units: metaid_0000059
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units def: metaid_0000058
length unit: length
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Lukas
    family: Endler
parameter: metaid_0000011
species: metaid_0000042
parameter: metaid_0000024
parameter: metaid_0000006
parameter: metaid_0000009
species: metaid_0000038
name: Chickarmane2006 - Stem cell switch reversible
modified:
  W3 CDTF: Wed Jun 05 17:59:33 BST 2013
parameter: metaid_0000014
parameter: metaid_0000030
is described by: http://identifiers.org/pubmed/16978048
parameter: metaid_0000033
species: metaid_0000047
species: metaid_0000037
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is version of: GO:0048863
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area units: metaid_0000005
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parameter: metaid_0000022
parameter: metaid_0000025
parameter: metaid_0000007
created:
  W3 CDTF: Tue Nov 25 17:19:46 GMT 2008
parameter: metaid_0000004
units def: metaid_0000059
creator:
  ORG:
    orgname: Lund Strategic Research Centre for Stem Cell Biology and Cell Therapy, Lund University, Sweden.
  n:
    given: Carsten
    family: Peterson
curated: true
parameter: metaid_0000005
parameter: metaid_0000012
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parameter: metaid_0000018
notes: Chickarmane2006 - Stem cell switch reversible Kinetic modeling approach of the transcriptional dynamics of the embryonic stem cell switch. This model is described in the article: Transcriptional dynamics of the embryonic stem cell switch. Chickarmane V, Troein C, Nuber UA, Sauro HM, Peterson C PLoS Computational Biology. 2006; 2(9):e123 Abstract: Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the transcription factors OCT4, SOX2, and NANOG. In addition to regulating each other through feedback loops, these genes also regulate downstream target genes involved in the maintenance and differentiation of embryonic stem cells. A search for the OCT4-SOX2-NANOG network motif in other species reveals that it is unique to mammals. With a kinetic modeling approach, we ascribe function to the observed OCT4-SOX2-NANOG network by making plausible assumptions about the interactions between the transcription factors at the gene promoter binding sites and RNA polymerase (RNAP), at each of the three genes as well as at the target genes. We identify a bistable switch in the network, which arises due to several positive feedback loops, and is switched on/off by input environmental signals. The switch stabilizes the expression levels of the three genes, and through their regulatory roles on the downstream target genes, leads to a binary decision: when OCT4, SOX2, and NANOG are expressed and the switch is on, the self-renewal genes are on and the differentiation genes are off. The opposite holds when the switch is off. The model is extremely robust to parameter changes. In addition to providing a self-consistent picture of the transcriptional circuit, the model generates several predictions. Increasing the binding strength of NANOG to OCT4 and SOX2, or increasing its basal transcriptional rate, leads to an irreversible bistable switch: the switc…
creator:
  ORG:
    orgname: EMBL-EBI
  n:
    given: Vijayalakshmi
    family: Chelliah
species: metaid_0000036
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time units: metaid_0000060
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is: MODEL7957907314
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parameter: metaid_0000023
units def: metaid_0000060
creator:
  ORG:
    orgname: Keck Graduate Institute, California
  n:
    given: Vijay
    family: Chickarmane
type: SBMLModel
species: metaid_0000045
species: metaid_0000039
occurs in: http://identifiers.org/taxonomy/9606
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parameter: metaid_0000013
species: metaid_0000044
parameter: metaid_0000008
parameter: metaid_0000026
occurs in: http://identifiers.org/taxonomy/10090
parameter: metaid_0000027
parameter: metaid_0000019

361900
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