Computational Biology/Gene Expression modeling/Stochastic Approach: Difference between revisions

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==Models described in literature==
==Models described in literature==


==Parameter estimation in E.Coli==
{| border="1" cellpadding="5" cellspacing="0" style="background:white; color:black; width:100%; center"
|-
! style="background:#efefef" | Parameter
! style="background:#efefef" | Estimate 
! style="background:#efefef" | Unit
! style="background:#efefef" | Description
! style="background:#efefef" | Reference
|-
| Nb Genes
| 4000
| n/a
|
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| Average Gene Length
| 1000
| nucleotides
| Average gene length in E.Coli
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| Nb RNAp/Cell
| 800
| n/a
| number of RNAp per E.Coli
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| RNAp footprint
| 60
| nucleotides
| footprint of RNAp when sitting on DNA
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| Transcription initiation rate
| 2-3
| nM/min
|
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| Transcription elongation rate
| 50
| nucleotides/seconde
| ...
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| mRNA half life
| 120
| seconde
| ...
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| Average mRNAs/gene
| 2-3
| n/a
| ...
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| Nb Ribosomes
| 12000
| n/a
| ...
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| Ribosome footprint
| 35
| nucleotides
| ...
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| Translation initiation rate
| 2-3
| mRNA/min
| ...
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| Translation elongation rate
| 60
| nucleotides/seconde
| ...
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| average Protein half-life
| 30
| min
| correspond to the dilution rate due to cell division
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
| average Proteins/gene
| 1000
| n/a
| ...
| [http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi E.Coli stats]
|-
|next parameter
| ...
| ...
| ...
| ...
|}


==Parameters used in literature==
==Parameters used in literature==
Line 17: Line 117:
! style="background:#efefef" | Author / Year  
! style="background:#efefef" | Author / Year  
! style="background:#efefef" | Reference
! style="background:#efefef" | Reference
|-
| Transcription initiation
| [0.1 - 0.14]
| min-1
| Plac/ara
| yes
| Golding et al, 2005
| [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WSN-4HTC1PP-J&_user=10&_coverDate=12%2F16%2F2005&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=70f66e87383e947c4c5a3e48c54b1d64  article]
|-
|-
| Transcription initiation
| Transcription initiation

Latest revision as of 08:21, 22 May 2007

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

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