Computational Biology/Gene Expression modeling/Stochastic Approach

Modeling resources dealing with Stochastic Gene Expression

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	[0.0025 - 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

• statistics about E.Coli

To do list

• include parameters from papers:
  • van Oudenaarden
  • Adam Arkin
  • Jeff Hasty
  • Ron Weiss
  • Dan Gillespie
  • Y Kaznessis