Difference between revisions of "Model Overview"

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(→‎Parameters for model reactions)
(→‎Parameters for model reactions)
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|rowspan="2" |[[Binding of R2 to A |Binding of R<sub>2</sub> to A]]
 
|rowspan="2" |[[Binding of R2 to A |Binding of R<sub>2</sub> to A]]
 
|<math>K_{d3}</math>  
 
|<math>K_{d3}</math>  
−
|
+
|10^{3}−10^{6}
 
|<math> nM </math>
 
|<math> nM </math>
−
|  
+
|<math>7 \cdot 10^{4}</math>
−
|
+
|10
−
|
+
|11.9714
−
|
+
|0.90284
 
|-
 
|-
 
|<math>k^{-}_{3}</math>  
 
|<math>k^{-}_{3}</math>  
−
|
+
|<math>60-6 \cdot 10^{4}</math>
 
|<math> min^{-1} </math>
 
|<math> min^{-1} </math>
−
|  
+
|2 \cdot 10^{4}
−
|
+
|2.5
−
|
+
|10.0888
−
|
+
|0.4305
 
|-
 
|-
 
|rowspan="2" |[[Binding of R2 to C |Binding of R<sub>2</sub> to C]]
 
|rowspan="2" |[[Binding of R2 to C |Binding of R<sub>2</sub> to C]]
 
|<math>K_{d4}</math>  
 
|<math>K_{d4}</math>  
−
|
+
|<math>10^{-2}-10^{-4}</math>
 
|<math> nM </math>
 
|<math> nM </math>
−
|  
+
|5
−
|
+
|1000
−
|
+
|5.3401
−
|
+
|1.9315
 
|-
 
|-
 
|<math>k^{-}_{4}</math>  
 
|<math>k^{-}_{4}</math>  
−
|
+
|3 \cdot 10^{-4}-126
 
|<math> min^{-1} </math>
 
|<math> min^{-1} </math>
−
|  
+
|1.3
−
|
+
|100
−
|
+
|2.4401
−
|
+
|1.4757
 
|-
 
|-
 
|rowspan="2" |[[Binding of A-R2 to OA' operator |Binding of A-R<sub>2</sub> to OA' operator]]
 
|rowspan="2" |[[Binding of A-R2 to OA' operator |Binding of A-R<sub>2</sub> to OA' operator]]
 
|<math>K_{d5}</math>  
 
|<math>K_{d5}</math>  
−
|
+
|0.005−5.8
 
|<math> nM </math>
 
|<math> nM </math>
−
|  
+
|0.15
−
|
+
|30
−
|
+
|−0.4648
−
|
+
|1.1968
 
|-
 
|-
 
|<math>k^{-}_{5}</math>  
 
|<math>k^{-}_{5}</math>  
−
|
+
|0.09−0.85
 
|<math> min^{-1} </math>
 
|<math> min^{-1} </math>
−
|  
+
|0.3
−
|
+
|4
−
|
+
|−0.8323
−
|
+
|0.6097
 
|-
 
|-
 
|[[Synthesis of C]]
 
|[[Synthesis of C]]
 
|<math>K_{C}</math>  
 
|<math>K_{C}</math>  
−
|
+
|0.003−0.01
 
|<math> min^{-1} </math>
 
|<math> min^{-1} </math>
−
|  
+
|0.005
−
|
+
|10
−
|
+
|−4.4832
−
|
+
|0.9028
 
|-
 
|-
 
|[[Transcription of r]]
 
|[[Transcription of r]]
−
|<math>K_{R}</math>  
+
|<math>T_{R}</math>  
−
|
+
|0.16−8.24
 
|<math> min^{-1} </math>
 
|<math> min^{-1} </math>
−
|  
+
|0.88
−
|
+
|10
−
|
+
|0.6873
−
|
+
|0.9028
 
|-
 
|-
 
|[[Transcription of a]]
 
|[[Transcription of a]]
−
|<math>K_{A}</math>  
+
|<math>T_{A}</math>  
−
|
+
|0.11−5.65
 
|<math> min^{-1} </math>
 
|<math> min^{-1} </math>
−
|  
+
|0.60
−
|
+
|10
−
|
+
|0.3043
−
|
+
|0.9028
 
|-
 
|-
 
|rowspan="2" |[[Antisense interaction between r and a]]
 
|rowspan="2" |[[Antisense interaction between r and a]]
 
|<math>K_{ar}</math>  
 
|<math>K_{ar}</math>  
−
|
+
|0.20−89
 
|<math> min^{-1} </math>
 
|<math> min^{-1} </math>
−
|  
+
|5
−
|
+
|10
−
|
+
|2.4246
−
|
+
|0.9028
 
|-
 
|-
 
|<math>k^{-}_{ar}</math>  
 
|<math>k^{-}_{ar}</math>  
−
|
+
|0.006−6
 
|<math> min^{-1} </math>
 
|<math> min^{-1} </math>
−
|  
+
|0.6
−
|
+
|10
−
|
+
|0.3043
−
|
+
|0.9028
 
|-
 
|-
 
|[[Translation of R]]
 
|[[Translation of R]]
 
|<math>P_{R}</math>  
 
|<math>P_{R}</math>  
−
|
+
|0.165−5.86
 
|<math> min^{-1} </math>
 
|<math> min^{-1} </math>
−
|  
+
|0.89
−
|
+
|10
−
|
+
|0.6873
−
|
+
|0.9028
 
|-
 
|-
 
|[[Translation of A]]
 
|[[Translation of A]]
 
|<math>P_{A}</math>  
 
|<math>P_{A}</math>  
−
|
+
|0.11−4
 
|<math> min^{-1} </math>
 
|<math> min^{-1} </math>
−
|  
+
|0.61
−
|
+
|10
−
|
+
|0.3208
−
|
+
|0.9028
 
|-
 
|-
 
|rowspan="2" |[[Formation of homo-dimer R2 |Formation of homo-dimer R<sub>2</sub>]]
 
|rowspan="2" |[[Formation of homo-dimer R2 |Formation of homo-dimer R<sub>2</sub>]]
 
|<math>K_{d6}</math>  
 
|<math>K_{d6}</math>  
−
|
+
|35.3−114
 
|<math> nM </math>
 
|<math> nM </math>
−
|  
+
|30
−
|
+
|30
−
|
+
|4.8335
−
|
+
|1.1968
 
|-
 
|-
 
|<math>k^{-}_{6}</math>  
 
|<math>k^{-}_{6}</math>  
−
|
+
|2.12−6.84
 
|<math> min^{-1} </math>
 
|<math> min^{-1} </math>
−
|  
+
|2
−
|
+
|30
−
|
+
|2.1255
−
|
+
|1.1968
 
|-
 
|-
 
|[[Degradation of r]]
 
|[[Degradation of r]]
 
|<math>d_{mR}</math>  
 
|<math>d_{mR}</math>  
−
|
+
|0.03−0.4
 
|<math>min^{-1}</math>
 
|<math>min^{-1}</math>
−
|  
+
|0.15
−
|
+
|3
−
|
+
|−1.6927
−
|
+
|0.5229
 
|-
 
|-
 
|[[Degradation of R]]
 
|[[Degradation of R]]
 
|<math>d_{R}</math>  
 
|<math>d_{R}</math>  
−
|
+
|<math>8.3 \cdot 10^{-4}- 0.0037</math>
 
|<math>min^{-1}</math>
 
|<math>min^{-1}</math>
−
|  
+
|<math>1.62 \cdot 10^{-3}</math>
−
|
+
|100
−
|
+
|−4.2475
−
|
+
|1.4757
 
|-
 
|-
 
|[[Degradation of R2 |Degradation of R<sub>2</sub>]]
 
|[[Degradation of R2 |Degradation of R<sub>2</sub>]]
 
|<math>d_{R_{2}}</math>  
 
|<math>d_{R_{2}}</math>  
−
|
+
|<math>8.3 \cdot 10^{-4}- 0.0037</math>
 
|<math>min^{-1}</math>
 
|<math>min^{-1}</math>
−
|  
+
|<math>1.62 \cdot 10^{-3}</math>
−
|
+
|100
−
|
+
|−4.2475
−
|
+
|1.4757
 
|-
 
|-
 
|[[Degradation of a]]
 
|[[Degradation of a]]
 
|<math>d_{mA}</math>  
 
|<math>d_{mA}</math>  
−
|
+
|0.03−0.4
 
|<math>min^{-1}</math>
 
|<math>min^{-1}</math>
−
|  
+
|0.15
−
|
+
|3
−
|
+
|−1.6927
−
|
+
|0.5229
 
|-
 
|-
 
|[[Degradation of A]]
 
|[[Degradation of A]]
 
|<math>d_{A}</math>  
 
|<math>d_{A}</math>  
−
|
+
|<math>8.3 \cdot 10^{-4}- 0.0037</math>
 
|<math>min^{-1}</math>
 
|<math>min^{-1}</math>
−
|  
+
|<math>1.62 \cdot 10^{-3}</math>
−
|
+
|100
−
|
+
|−4.2475
−
|
+
|1.4757
 
|-
 
|-
 
|[[Degradation of C]]
 
|[[Degradation of C]]
 
|<math>d_{C}</math>  
 
|<math>d_{C}</math>  
−
|
+
|<math>2.86 \cdot 10^{-4}- 2 \cdot 10^{-2}</math>
 
|<math>min^{-1}</math>
 
|<math>min^{-1}</math>
−
|  
+
|2 \cdot 10^{-4}
−
|
+
|10
−
|
+
|−7.7021
−
|
+
|0.9028
 
|-
 
|-
 
|[[Degradation of C2-R2 |Degradation of C<sub>2</sub>-R<sub>2</sub>]]
 
|[[Degradation of C2-R2 |Degradation of C<sub>2</sub>-R<sub>2</sub>]]
 
|<math>d_{CR}</math>  
 
|<math>d_{CR}</math>  
−
|
+
|<math>8.3 \cdot 10^{-4}- 0.0037</math>
 
|<math>min^{-1}</math>
 
|<math>min^{-1}</math>
−
|  
+
|<math>1.62 \cdot 10^{-3}</math>
−
|
+
|100
−
|
+
|−4.2475
−
|
+
|1.4757
 
|-
 
|-
 
|[[Degradation of A-R2 |Degradation of A-R<sub>2</sub>]]
 
|[[Degradation of A-R2 |Degradation of A-R<sub>2</sub>]]
 
|<math>d_{AR}</math>  
 
|<math>d_{AR}</math>  
−
|
+
|<math>8.3 \cdot 10^{-4}- 0.0037</math>
 
|<math>min^{-1}</math>
 
|<math>min^{-1}</math>
−
|  
+
|<math>1.62 \cdot 10^{-3}</math>
−
|
+
|100
−
|
+
|−4.2475
−
|
+
|1.4757
 
|-
 
|-
 
|[[Degradation of r-a]]
 
|[[Degradation of r-a]]
 
|<math>d_{mAR}</math>  
 
|<math>d_{mAR}</math>  
−
|
+
|0.35−34.7
 
|<math>min^{-1}</math>
 
|<math>min^{-1}</math>
−
|  
+
|5
−
|
+
|6
−
|
+
|2.1670
−
|
+
|0.7467
 
|-
 
|-
 
|[[Diffusion of C and Ce |Diffusion of C and C<sub>e</sub>]]
 
|[[Diffusion of C and Ce |Diffusion of C and C<sub>e</sub>]]
 
|<math>D</math>  
 
|<math>D</math>  
−
|
+
|0.1−24
 
|<math>min^{-1}</math>
 
|<math>min^{-1}</math>
−
|  
+
|8
−
|
+
|2
−
|
+
|2.1267
−
|
+
|0.2174
 
|-
 
|-
 
|[[Degradation of Ce]]
 
|[[Degradation of Ce]]
 
|<math>d_{C}</math>  
 
|<math>d_{C}</math>  
−
|
+
|<math>2.86 \cdot 10^{-4}- 2 \cdot 10^{-2}</math>
 
|<math>min^{-1}</math>
 
|<math>min^{-1}</math>
−
|  
+
|2 \cdot 10^{-4}
−
|
+
|10
−
|
+
|−7.7021
−
|
+
|0.9028
 
|-
 
|-
 
|[[Cellular growth]]
 
|[[Cellular growth]]
 
|<math>μ</math>  
 
|<math>μ</math>  
−
|
+
|0.0004−0.011
 
|<math>min^{-1}</math>
 
|<math>min^{-1}</math>
−
|  
+
|0.001
−
|
+
|10
−
|
+
|−6.0926
−
|
+
|0.9028
 
|}
 
|}
  

Revision as of 06:33, 19 October 2015

Go back to overview
About this image

Parameters for model reactions

Reaction Parameter Value Units Distribution

Mode

Confidence

Interval Factor

Location

parameter (μ)

Scale

parameter (σ)

Binding of R2 to OR operator K_{d1} 0.005−5.8 nM 0.15 20 −0.7010 1.094
k^{-}_{1} 0.09−0.85 min^{-1} 0.3 3.5 −0.8890 0.5612
Binding of R2 to OA operator K_{d2} 0.005−5.8 nM 0.15 20 −0.7010 1.094
k^{-}_{2} 0.09−0.85 min^{-1} 0.3 3.5 −0.8890 0.5612
Binding of R2 to A K_{d3} 10^{3}−10^{6} nM Failed to parse (Cannot store math image on filesystem.): 7 \cdot 10^{4} 10 11.9714 0.90284
k^{-}_{3} 60-6 \cdot 10^{4} min^{-1} 2 \cdot 10^{4} 2.5 10.0888 0.4305
Binding of R2 to C K_{d4} Failed to parse (Cannot store math image on filesystem.): 10^{-2}-10^{-4} nM 5 1000 5.3401 1.9315
k^{-}_{4} 3 \cdot 10^{-4}-126 min^{-1} 1.3 100 2.4401 1.4757
Binding of A-R2 to OA' operator K_{d5} 0.005−5.8 nM 0.15 30 −0.4648 1.1968
k^{-}_{5} 0.09−0.85 min^{-1} 0.3 4 −0.8323 0.6097
Synthesis of C K_{C} 0.003−0.01 min^{-1} 0.005 10 −4.4832 0.9028
Transcription of r T_{R} 0.16−8.24 min^{-1} 0.88 10 0.6873 0.9028
Transcription of a T_{A} 0.11−5.65 min^{-1} 0.60 10 0.3043 0.9028
Antisense interaction between r and a K_{ar} 0.20−89 min^{-1} 5 10 2.4246 0.9028
k^{-}_{ar} 0.006−6 min^{-1} 0.6 10 0.3043 0.9028
Translation of R P_{R} 0.165−5.86 min^{-1} 0.89 10 0.6873 0.9028
Translation of A P_{A} 0.11−4 min^{-1} 0.61 10 0.3208 0.9028
Formation of homo-dimer R2 K_{d6} 35.3−114 nM 30 30 4.8335 1.1968
k^{-}_{6} 2.12−6.84 min^{-1} 2 30 2.1255 1.1968
Degradation of r d_{mR} 0.03−0.4 min^{-1} 0.15 3 −1.6927 0.5229
Degradation of R d_{R} 8.3 \cdot 10^{-4}- 0.0037 min^{-1} Failed to parse (Cannot store math image on filesystem.): 1.62 \cdot 10^{-3} 100 −4.2475 1.4757
Degradation of R2 d_{R_{2}} 8.3 \cdot 10^{-4}- 0.0037 min^{-1} Failed to parse (Cannot store math image on filesystem.): 1.62 \cdot 10^{-3} 100 −4.2475 1.4757
Degradation of a d_{mA} 0.03−0.4 min^{-1} 0.15 3 −1.6927 0.5229
Degradation of A d_{A} 8.3 \cdot 10^{-4}- 0.0037 min^{-1} Failed to parse (Cannot store math image on filesystem.): 1.62 \cdot 10^{-3} 100 −4.2475 1.4757
Degradation of C d_{C} Failed to parse (Cannot store math image on filesystem.): 2.86 \cdot 10^{-4}- 2 \cdot 10^{-2} min^{-1} 2 \cdot 10^{-4} 10 −7.7021 0.9028
Degradation of C2-R2 d_{CR} 8.3 \cdot 10^{-4}- 0.0037 min^{-1} Failed to parse (Cannot store math image on filesystem.): 1.62 \cdot 10^{-3} 100 −4.2475 1.4757
Degradation of A-R2 d_{AR} 8.3 \cdot 10^{-4}- 0.0037 min^{-1} Failed to parse (Cannot store math image on filesystem.): 1.62 \cdot 10^{-3} 100 −4.2475 1.4757
Degradation of r-a d_{mAR} 0.35−34.7 min^{-1} 5 6 2.1670 0.7467
Diffusion of C and Ce D 0.1−24 min^{-1} 8 2 2.1267 0.2174
Degradation of Ce d_{C} Failed to parse (Cannot store math image on filesystem.): 2.86 \cdot 10^{-4}- 2 \cdot 10^{-2} min^{-1} 2 \cdot 10^{-4} 10 −7.7021 0.9028
Cellular growth Failed to parse (PNG conversion failed; check for correct installation of latex and dvipng (or dvips + gs + convert)): μ 0.0004−0.011 min^{-1} 0.001 10 −6.0926 0.9028

Parameters for cell colony growth

Parameter Value Units
Failed to parse (PNG conversion failed; check for correct installation of latex and dvipng (or dvips + gs + convert)): τ 63-1732 min
Failed to parse (PNG conversion failed; check for correct installation of latex and dvipng (or dvips + gs + convert)): λ 0.8 -
V_{0} 1.2 μm^{3}
V_{tot} 2 \cdot 10^{−4} μl
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