Computational Biology/Gene Expression modeling/Stochastic Approach
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Modeling resources dealing with Stochastic Gene Expression
Models described in literature
Parameter estimation in E.Coli
| Parameter | Estimate | Unit | Description | Reference |
|---|---|---|---|---|
| Nb Genes | 4000 | n/a | E.Coli stats | |
| Average Gene Length | 1000 | nucleotides | Average gene length in E.Coli | E.Coli stats |
| Nb RNAp/Cell | 800 | n/a | number of RNAp per E.Coli | E.Coli stats |
| RNAp footprint | 60 | nucleotides | footprint of RNAp when sitting on DNA | E.Coli stats |
| Transcription initiation rate | 2-3 | nM/min | E.Coli stats | |
| Transcription elongation rate | 50 | nucleotides/seconde | ... | E.Coli stats |
| mRNA half life | 120 | seconde | ... | E.Coli stats |
| Average mRNAs/gene | 2-3 | n/a | ... | E.Coli stats |
| Nb Ribosomes | 12000 | n/a | ... | E.Coli stats |
| Ribosome footprint | 35 | nucleotides | ... | E.Coli stats |
| Translation initiation rate | 2-3 | mRNA/min | ... | E.Coli stats |
| Translation elongation rate | 60 | nucleotides/seconde | ... | E.Coli stats |
| average Protein half-life | 30 | min | correspond to the dilution rate due to cell division | E.Coli stats |
| average Proteins/gene | 1000 | n/a | ... | E.Coli stats |
| next parameter | ... | ... | ... | ... |
Parameters used in literature
Transcription related events
| Event modeled | Value / Range | Unit | Part / Organism | Experimental validation | Author / Year | Reference |
|---|---|---|---|---|---|---|
| Transcription initiation | [0.1 - 0.14] | min-1 | Plac/ara | yes | Golding et al, 2005 | article |
| 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 |
Translation related events
| 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:
