Computational Biology/Gene Expression modeling/Stochastic Approach: Difference between revisions
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(New page: __NOTOC__ =Modeling resources dealing with Stochastic Gene Expression= ==Models described in literature== ==Parameters used in literature== ===Transcription related events=== ===mRNA...) |
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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== | ||
===Transcription related events=== | ===Transcription related events=== | ||
{| border="1" cellpadding="5" cellspacing="0" style="background:white; color:black; width:100%; center" | |||
|- | |||
! style="background:#efefef" | Event modeled | |||
! style="background:#efefef" | Value / Range | |||
! style="background:#efefef" | Unit | |||
! style="background:#efefef" | Part / Organism | |||
! style="background:#efefef" | Experimental validation | |||
! style="background:#efefef" | Author / Year | |||
! 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 | |||
| [0.0025 - 0.2] | |||
| s-1 | |||
| generic | |||
| no | |||
| Thattai et al, 2001 | |||
| [http://www.pnas.org/cgi/content/abstract/98/15/8614 article] | |||
|- | |||
|interval between transcription initiations | |||
| 3.3 | |||
| s | |||
| Lac Operon, E.Coli | |||
| Yes | |||
| Kennell et al, 1977 | |||
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4DN8XFK-S6&_user=217827&_coverDate=07%2F25%2F1977&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000011279&_version=1&_urlVersion=0&_userid=217827&md5=ce08194a572e3762fb0688ac473ba4ae article] | |||
|- | |||
|next event | |||
| [0.01 - 0.1] | |||
| s-1 | |||
| not defined | |||
| no | |||
| Dr Doc | |||
| link | |||
|} | |||
===mRNA degradation=== | ===mRNA degradation=== | ||
{| border="1" cellpadding="5" cellspacing="0" style="background:white; color:black; width:100%; center" | |||
|- | |||
! style="background:#efefef" | Event modeled | |||
! style="background:#efefef" | Value / Range | |||
! style="background:#efefef" | Unit | |||
! style="background:#efefef" | Part / Organism | |||
! style="background:#efefef" | Experimental validation | |||
! style="background:#efefef" | Author / Year | |||
! style="background:#efefef" | Reference | |||
|- | |||
| mRNA half-life | |||
| 2 | |||
| min | |||
| generic | |||
| no | |||
| Thattai et al, 2001 | |||
| [http://www.pnas.org/cgi/content/abstract/98/15/8614 article] | |||
|- | |||
|next event | |||
| 0.01 - 0.1 | |||
| s-1 | |||
| not defined | |||
| no | |||
| Dr Doc | |||
| link | |||
|} | |||
===Translation related events=== | ===Translation related events=== | ||
{| border="1" cellpadding="5" cellspacing="0" style="background:white; color:black; width:100%; center" | |||
|- | |||
! style="background:#efefef" | Event modeled | |||
! style="background:#efefef" | Value / Range | |||
! style="background:#efefef" | Unit | |||
! style="background:#efefef" | Part / Organism | |||
! style="background:#efefef" | Experimental validation | |||
! style="background:#efefef" | Author / Year | |||
! style="background:#efefef" | Reference | |||
|- | |||
| Translation initiation | |||
| [0.028-0.231] | |||
| | |||
| generic | |||
| no | |||
| Thattai et al, 2001 | |||
| [http://www.pnas.org/cgi/content/abstract/98/15/8614 article] | |||
|- | |||
|Translation burst | |||
| 40 | |||
| molecules/mRNA | |||
| Lac Operon, E.Coli | |||
| Yes | |||
| Kennell et al, 1977 | |||
|[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WK7-4DN8XFK-S6&_user=217827&_coverDate=07%2F25%2F1977&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000011279&_version=1&_urlVersion=0&_userid=217827&md5=ce08194a572e3762fb0688ac473ba4ae article] | |||
|- | |||
|next event | |||
| 0.01 - 0.1 | |||
| s-1 | |||
| not defined | |||
| no | |||
| Dr Doc | |||
| link | |||
|} | |||
===Protein degradation=== | ===Protein degradation=== | ||
{| border="1" cellpadding="5" cellspacing="0" style="background:white; color:black; width:100%; center" | |||
|- | |||
! style="background:#efefef" | Event modeled | |||
! style="background:#efefef" | Value / Range | |||
! style="background:#efefef" | Unit | |||
! style="background:#efefef" | Part / Organism | |||
! style="background:#efefef" | Experimental validation | |||
! style="background:#efefef" | Author / Year | |||
! style="background:#efefef" | Reference | |||
|- | |||
| Protein half-life | |||
| [15-120] | |||
| min | |||
| generic | |||
| no | |||
| Thattai et al, 2001 | |||
| [http://www.pnas.org/cgi/content/abstract/98/15/8614 article] | |||
|- | |||
|next event | |||
| 0.01 - 0.1 | |||
| s-1 | |||
| not defined | |||
| no | |||
| Dr Doc | |||
| link | |||
|} | |||
==Interesting links== | ==Interesting links== | ||
*[http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi statistics about E.Coli] | *[http://redpoll.pharmacy.ualberta.ca/CCDB/cgi-bin/STAT_NEW.cgi statistics about E.Coli] | ||
==To do list== | |||
*include parameters from papers: | |||
**[http://scholar.google.com/scholar?hl=en&q=van+Oudenaarden&spell=1 van Oudenaarden] | |||
**[http://scholar.google.com/scholar?hl=en&lr=&q=adam+arkin&btnG=Search Adam Arkin] | |||
**[http://scholar.google.com/scholar?hl=en&lr=&q=jeff+hasty&btnG=Search Jeff Hasty] | |||
**[http://scholar.google.com/scholar?hl=en&lr=&q=Ron+weiss&btnG=Search Ron Weiss] | |||
**[http://scholar.google.com/scholar?hl=en&lr=&q=Dan+Gillespie&btnG=Search Dan Gillespie] | |||
**[http://scholar.google.com/scholar?hl=en&lr=&q=Y+Kaznessis&btnG=Search Y Kaznessis] |
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
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: