Difference between revisions of "Model Overview"
(→List of Model Reactions) |
(→Parameters for model reactions) |
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Line 86: | Line 86: | ||
! Distribution | ! Distribution | ||
Mode | Mode | ||
− | ! | + | ! Spread |
− | |||
! Location | ! Location | ||
parameter (μ) | parameter (μ) | ||
Line 98: | Line 97: | ||
|<math> nM </math> | |<math> nM </math> | ||
|0.299 | |0.299 | ||
− | | | + | |6.8 |
− | |0. | + | |0.15471 |
− | |1. | + | |1.1661 |
|- | |- | ||
|<math>k^{-}_{1}, k^{-}_{7}</math> | |<math>k^{-}_{1}, k^{-}_{7}</math> | ||
Line 106: | Line 105: | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
|0.489 | |0.489 | ||
− | | | + | |1.98 |
− | |−0. | + | |−0.37642 |
− | |0. | + | |0.58225 |
|- | |- | ||
|rowspan="2" |[[Binding of R2 to OA operator |Binding of R<sub>2</sub> to OA operator]] | |rowspan="2" |[[Binding of R2 to OA operator |Binding of R<sub>2</sub> to OA operator]] | ||
Line 115: | Line 114: | ||
|<math> nM </math> | |<math> nM </math> | ||
|0.299 | |0.299 | ||
− | | | + | |6.8 |
− | |0. | + | |0.15471 |
− | |1. | + | |1.1661 |
|- | |- | ||
|<math>k^{-}_{2},k^{-}_{8}</math> | |<math>k^{-}_{2},k^{-}_{8}</math> | ||
Line 123: | Line 122: | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
|0.489 | |0.489 | ||
− | | | + | |1.98 |
− | |−0. | + | |−0.37642 |
− | |0. | + | |0.58225 |
|- | |- | ||
|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]] | ||
Line 131: | Line 130: | ||
|<math>10^{4}−10^{6}</math> | |<math>10^{4}−10^{6}</math> | ||
|<math> nM </math> | |<math> nM </math> | ||
− | |<math> | + | |<math>9.9 \cdot 10^{4}</math> |
− | | | + | |10.02 |
− | | | + | |13.192 |
− | |1. | + | |1.2977 |
|- | |- | ||
|<math>k^{-}_{3}</math> | |<math>k^{-}_{3}</math> | ||
|<math>38.3-4.46 \cdot 10^{6}</math> | |<math>38.3-4.46 \cdot 10^{6}</math> | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
− | | | + | |N/A |
− | | | + | |N/A |
− | | | + | |9.9423 |
− | |1. | + | |1.5503 |
|- | |- | ||
|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]] | ||
Line 148: | Line 147: | ||
|<math>0.0011-10400</math> | |<math>0.0011-10400</math> | ||
|<math> nM </math> | |<math> nM </math> | ||
− | | | + | |N/A |
− | | | + | |N/A |
− | | | + | |5.9389 |
− | |2. | + | |2.3412 |
|- | |- | ||
|<math>k^{-}_{4}</math> | |<math>k^{-}_{4}</math> | ||
|<math>3 \cdot 10^{-4}-126</math> | |<math>3 \cdot 10^{-4}-126</math> | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
− | |0. | + | |0.816 |
− | | | + | |244 |
− | | | + | |4.2872 |
− | |2. | + | |2.119 |
|- | |- | ||
|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]] | ||
Line 166: | Line 165: | ||
|<math> nM </math> | |<math> nM </math> | ||
|0.299 | |0.299 | ||
− | | | + | |6.8 |
− | |0. | + | |0.15471 |
− | |1. | + | |1.1661 |
|- | |- | ||
|<math>k^{-}_{5},k^{-}_{9},k^{-}_{10},k^{-}_{11},k^{-}_{12}</math> | |<math>k^{-}_{5},k^{-}_{9},k^{-}_{10},k^{-}_{11},k^{-}_{12}</math> | ||
Line 174: | Line 173: | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
|0.489 | |0.489 | ||
− | | | + | |1.98 |
− | |−0. | + | |−0.37642 |
− | |0. | + | |0.58225 |
|- | |- | ||
|[[Synthesis of C]] | |[[Synthesis of C]] | ||
|<math>K_{C}</math> | |<math>K_{C}</math> | ||
− | |0. | + | |0.00315−85.5 |
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
− | |0. | + | |0.094 |
− | | | + | |60.49 |
− | | | + | |0.87914 |
− | | | + | |1.8017 |
|- | |- | ||
|rowspan="3" |[[Transcription of r]] | |rowspan="3" |[[Transcription of r]] | ||
Line 192: | Line 191: | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
|0.8346 | |0.8346 | ||
− | | | + | |3.55 |
− | |0. | + | |0.63056 |
− | |0. | + | |0.90076 |
|- | |- | ||
|<math>k_{F}</math> | |<math>k_{F}</math> | ||
|18.2−33 | |18.2−33 | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
− | |20. | + | |20.7 |
− | |1. | + | |1.34 |
− | |3. | + | |3.1107 |
− | |0. | + | |0.28276 |
|- | |- | ||
|<math>k_{onR}</math> | |<math>k_{onR}</math> | ||
Line 208: | Line 207: | ||
|<math> min^{-1} </math> | |<math> min^{-1} </math> | ||
|0.867 | |0.867 | ||
− | | | + | |4.09 |
− | |0. | + | |0.78694 |
− | |1. | + | |0.96428 |
+ | |- | ||
+ | |rowspan="3" |[[Transcription of a]] | ||
+ | |<math>\Omega_{A_{basal}}</math> | ||
+ | |0.001−0.2 | ||
+ | |<math> min^{-1} </math> | ||
+ | |0.0037 | ||
+ | |10.93 | ||
+ | |−3.8324 | ||
+ | |1.3259 | ||
|- | |- | ||
− | |||
|<math>\Omega_{A}</math> | |<math>\Omega_{A}</math> | ||
|0.11−5.65 | |0.11−5.65 |
Revision as of 17:24, 23 November 2017
Contents
List of Model Reactions
*1 Reactions taking place only in the scenario which includes the activating complex
*2 Reactions taking place only in the scenario which includes the antisense RNA interactions
Reactions |
---|
*1
*1 *1 *1 *1 *1
*1 *2
*1 *2
|
Parameters for model reactions
Reaction | Parameter | Value | Units | Distribution
Mode |
Spread | Location
parameter (μ) |
Scale
parameter (σ) |
---|---|---|---|---|---|---|---|
Binding of R2 to OR operator | 0.005−5.8 | 0.299 | 6.8 | 0.15471 | 1.1661 | ||
0.09−0.846 | 0.489 | 1.98 | −0.37642 | 0.58225 | |||
Binding of R2 to OA operator | 0.005−5.8 | 0.299 | 6.8 | 0.15471 | 1.1661 | ||
0.09−0.846 | 0.489 | 1.98 | −0.37642 | 0.58225 | |||
Binding of R2 to A | 10.02 | 13.192 | 1.2977 | ||||
N/A | N/A | 9.9423 | 1.5503 | ||||
Binding of R2 to C | N/A | N/A | 5.9389 | 2.3412 | |||
0.816 | 244 | 4.2872 | 2.119 | ||||
Binding of A-R2 to OA' operator | 0.005−5.8 | 0.299 | 6.8 | 0.15471 | 1.1661 | ||
0.09−0.846 | 0.489 | 1.98 | −0.37642 | 0.58225 | |||
Synthesis of C | 0.00315−85.5 | 0.094 | 60.49 | 0.87914 | 1.8017 | ||
Transcription of r | 0.16−8.24 | 0.8346 | 3.55 | 0.63056 | 0.90076 | ||
18.2−33 | 20.7 | 1.34 | 3.1107 | 0.28276 | |||
0.0518-14.5 | 0.867 | 4.09 | 0.78694 | 0.96428 | |||
Transcription of a | 0.001−0.2 | 0.0037 | 10.93 | −3.8324 | 1.3259 | ||
0.11−5.65 | 0.57 | 12.5 | 0.354505 | 0.95491 | |||
0.039-8.82 | 0.587 | 15 | 0.47762 | 1.0048 | |||
Antisense interaction between r and a | 0.4−89 | 7.8 | 52.8 | 3.7933 | 1.3186 | ||
0.006−6 | 0.22 | 23.2 | −0.24716 | 1.1192 | |||
Translation of R | 0.165−5.86 | 0.74 | 10.3 | 0.50964 | 0.89756 | ||
Translation of A | 0.11−4 | 0.51 | 10.3 | 0.13413 | 0.89936 | ||
Formation of homo-dimer R2 | 2.58-42.9 | 30 | 30 | 4.8018 | 1.1835 | ||
0.144-51.2 | 2 | 30 | 2.094 | 1.1835 | |||
Degradation of r | 0.03−0.365 | 0.14 | 4.24 | −1.5762 | 0.62077 | ||
Degradation of R | 2.5 | −6.2752 | 0.4285 | ||||
Degradation of R2 | 2.5 | −6.2752 | 0.4285 | ||||
Degradation of a | 0.03−0.365 | 0.14 | 4.24 | −1.5762 | 0.62077 | ||
Degradation of A | 2.5 | −6.2752 | 0.4285 | ||||
Degradation of C | 25.8 | −4.4205 | 1.1461 | ||||
Degradation of C2-R2 | 2.5 | −6.2752 | 0.4285 | ||||
Degradation of A-R2 | 2.5 | −6.2752 | 0.4285 | ||||
Degradation of r-a | 0.35−69.3 | 0.739 | 200.4 | 2.2813 | 1.6074 | ||
Diffusion of C and Ce | 0.1−24 | 2.8 | 18.2 | 2.1457 | 1.0564 | ||
Degradation of Ce | 25.8 | −4.4205 | 1.1461 | ||||
Cellular growth | Failed to parse (PNG conversion failed; check for correct installation of latex and dvipng (or dvips + gs + convert)): μ | 0.0004−0.0107 | 0.0022 | 7.5 | −5.4517 | 0.80808 |
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 | ||
Failed to parse (PNG conversion failed; check for correct installation of latex and dvipng (or dvips + gs + convert)): λ | ||
Initial concentrations of species
Species | Initial concentration | Units | Compartment |
---|---|---|---|
OR | 0.9592 | Cell | |
OA | 0.9592 | Cell | |
OR-R2 | 0 | Cell | |
OA-R2 | 0 | Cell | |
OA'-AR2 | 0 | Cell | |
r | 0 | Cell | |
a | 0 | Cell | |
r-a | 0 | Cell | |
R | 0 | Cell | |
R2 | 0 | Cell | |
A | 0 | Cell | |
C | 0 | Cell | |
AR2 | 0 | Cell | |
C2R2 | 0 | Cell | |
Ce | 0 | Environment |