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
| 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
|
| 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:
