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

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