Computational Biology/Gene Expression modeling/Stochastic Approach
From OpenWetWare
Modeling resources dealing with Stochastic Gene Expression
Models described in literature
Parameter estimation in E.Coli
| Parameter | Estimate | Unit | Description | Reference |
|---|---|---|---|---|
| Nb Genes | ... | s-1 | ... | E.Coli stats |
| Nb RNAp | ... | s-1 | ... | E.Coli stats |
| RNAp footprint | ... | s-1 | ... | E.Coli stats |
| Transcription initiation rate | ... | s-1 | ... | E.Coli stats |
| Transcription elongation rate | ... | s-1 | ... | E.Coli stats |
| mRNA half life | ... | s-1 | ... | E.Coli stats |
| Average mRNAs/Cell | ... | s-1 | ... | E.Coli stats |
| Nb Ribosomes | ... | s-1 | ... | E.Coli stats |
| Ribosome footprint | ... | s-1 | ... | E.Coli stats |
| Translation initiation rate | ... | s-1 | ... | E.Coli stats |
| Translation elongation rate | ... | s-1 | ... | E.Coli stats |
| average Protein half-life | ... | s-1 | ... | E.Coli stats |
| average Proteins/Cell | ... | s-1 | ... | E.Coli stats |
| next event | [0.01 - 0.1] | s-1 | not defined | link |
Parameters used in literature
| Event modeled | Value / Range | Unit | Part / Organism | Experimental validation | Author / Year | Reference |
|---|---|---|---|---|---|---|
| Transcription initiation | [0.0025 - 0.2] | s-1 | generic | no | Thattai et al, 2001 | article |
| interval between transcription initiations | 3.3 | s | Lac Operon, E.Coli | Yes | Kennell et al, 1977 | article |
| next event | [0.01 - 0.1] | s-1 | not defined | no | Dr Doc | link |
mRNA degradation
| Event modeled | Value / Range | Unit | Part / Organism | Experimental validation | Author / Year | Reference |
|---|---|---|---|---|---|---|
| mRNA half-life | 2 | min | generic | no | Thattai et al, 2001 | article |
| next event | 0.01 - 0.1 | s-1 | not defined | no | Dr Doc | link |
| Event modeled | Value / Range | Unit | Part / Organism | Experimental validation | Author / Year | Reference |
|---|---|---|---|---|---|---|
| Translation initiation | [0.028-0.231] | generic | no | Thattai et al, 2001 | article | |
| Translation burst | 40 | molecules/mRNA | Lac Operon, E.Coli | Yes | Kennell et al, 1977 | article |
| next event | 0.01 - 0.1 | s-1 | not defined | no | Dr Doc | link |
Protein degradation
| Event modeled | Value / Range | Unit | Part / Organism | Experimental validation | Author / Year | Reference |
|---|---|---|---|---|---|---|
| Protein half-life | [15-120] | min | generic | no | Thattai et al, 2001 | article |
| next event | 0.01 - 0.1 | s-1 | not defined | no | Dr Doc | link |
Interesting links
To do list
- include parameters from papers:
